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Interactions between oceanic and atmospheric processes within coral reefs can significantly alter local-scale ( 60%) over most of this system; however, the bleaching patterns were not uniform. Little is known about the processes governing thermodynamic variability within atolls, particularly those that are dominated by large amplitude tides. Here, we identify three mechanisms at Scott Reef that alleviated heat stress during the marine heatwave in 2016: (1) the cool wake of a tropical cyclone that induced temperature drops of 1.3 °C over a period of 8 days; (2) air–sea heat fluxes that interacted with the reef morphology during neap tides at one of the atolls to reduce water temperatures by up to 2.9 °C; (3) internal tidal processes that forced deeper and cooler water (up to 2.7 °C) into some sections of the shallow reefs. The latter two processes created localized areas of reduced temperatures that led to lower incidences of coral bleaching for parts of the reef. We predict these processes are likely to occur in other similar tide-dominated reef environments worldwide. Identifying locations where physical processes reduce heat stress will likely be critical for coral reefs in the future, by maintaining communities that can help facilitate local recovery of reefs following bleaching events that are expected to increase in frequency and severity in the coming decades.

International audience; The rates of water exchange between coastal reef systems and the surrounding ocean are key physical drivers of water quality and reef ecosystems. It is generally assumed that water exiting a reef system through reef channels is predominantly replaced by 'new' water from offshore. However, exiting water may also recirculate back into the reef system reducing the rate of exchange between the reef and the ocean, which has implications for reef water temperatures, nutrient fluxes and population connectivity. To quantify flow re-entrainment at a rocky reef site in southwestern Australia, flow patterns were measured with GPS-tracked drifters during a two-week field experiment. The field observations were extended via a set of idealized numerical experiments to determine the effect of variable oceanic forcing and reef geometry on flow re-entrainment. The observations demonstrate that re-entrainment can vary significantly and the numerical results support the hypothesis that re-entrainment increases with increasing offshore wave height, increasing alongshore currents outside of the reef, and decreasing reef channel spacing but is largely not impacted by reef roughness. Reentrainment was correlated with a predictor variable R, which is a measure of wave forcing versus the total offshore flow cross-section, and alongshore currents outside the reef. For large values of R and strong alongshore currents, flow re-entrainment increases the effective flushing time by a factor of three or more. The results suggest that flow re-entrainment may be particularly important in small-scale reef systems or reefs exposed to an energetic wave climate and/or strong alongshore currents.

Coral reefs are an important source of sediment for reef-lined coasts and help to maintain beaches by providing protection though dissipation of wave energy. Understanding the mechanisms that deliver sediment to the coast from coral reefs and quantifying the total volume of sediment generated at coral reefs are critical for projecting future coastal change. A month-long hydrodynamics and sediment transport study on a fringing reef/lagoon complex in Western Australia indicates that lower frequency wave energy constituents are important to the total bedload transport of sediment across the reef flat and lagoon to the shoreline. The reef flat and the lagoon are characterized by distinctly different transport regimes, resulting in an offset in the timing of bedform migration between the two. Short-term storage of sediment occurs on the reef flat, which is subsequently transported into the lagoon when offshore wave heights increase and strong currents due to wave breaking at the reef crest develop. This sudden influx of sediment is correlated with an increase in bedform migration rates in the lagoon. Infragravity wave energy on the reef flat and lagoon make an important contribution to the migration of bedforms and resultant bedload transport. Given the complexity of the hydrodynamics of fringing reefs, the transfer of energy to lower frequency bands, as well as accurate estimates of sources and sinks of sediment, must but considered in order to correctly model the transport of sediment from the reef to the coast.

Pocket beaches bound by headlands or other geologic features are common worldwide and experience constrained alongshore transport that influences their morphological changes. Pocket beaches fringed by shallow reefs have not been well-studied, yet can be commonly found throughout temperate and tropical regions. The presence of a reef is expected to drive distinct hydrodynamic processes and shoreline responses to offshore waves and water levels, which is investigated in this study. To examine the drivers of shoreline variability, a 20-month field study was conducted on a reef-fringed pocket beach in southwestern Australia (Gnarabup Beach), using a series of in situ wave and water level observations, topographic surveys, as well as video shoreline monitoring. The results indicate that the beach as a whole (alongshore averaged) was in a mostly stable state. However, we observed substantial spatial variability of the local shorelines in response to offshore wave and water levels across a range of time-scales (from individual storms to the seasonal cycle). We observed local regions of beach rotation within cells that were partitioned by the headlands and offshore reefs. The shoreline response was also dictated by the combination of offshore waves and water level which varied seasonally, with the shoreline generally eroding with lower water levels for the same wave height. Despite the contrasting responses in different alongshore locations of the beach, the overall beach volume of the pocket beach was largely conserved.

Tropical coral reef-lined coasts are exposed to storm wave-driven flooding. In the future, flood events during storms are expected to occur more frequently and to be more severe due to sea-level rise, changes in wind and weather patterns, and the deterioration of coral reefs. Hence, disaster managers and coastal planners are in urgent need of decision-support tools. In the short-term, these tools can be applied in Early Warning Systems (EWS) that can help to prepare for and respond to impending storm-driven flood events. In the long-term, future scenarios of flooding events enable coastal communities and managers to plan and implement adequate risk-reduction strategies. Modeling tools that are used in currently available coastal flood EWS and future scenarios have been developed for open-coast sandy shorelines, which have only limited applicability for coral reef-lined shorelines. The tools need to be able to predict local sea levels, offshore waves, as well as their nearshore transformation over the reefs, and translate this information to onshore flood levels. In addition, future scenarios require long-term projections of coral reef growth, reef composition, and shoreline change. To address these challenges, we have formed the UFORiC (Understanding Flooding of Reef-lined Coasts) working group that outlines its perspectives on data and model requirements to develop EWS for storms and scenarios specific to coral reef-lined coastlines. It reviews the state-of-the-art methods that can currently be incorporated in such systems and provides an outlook on future improvements as new data sources and enhanced methods become available.

The distant passage of an intense and large Category 3 Tropical Cyclone (TC) generated highly energetic surface waves in a large region across the Australian North West Shelf (NWS). Two sites on the continental shelf experienced maximum significant wave heights of up to 10 m with near-bed wave orbital velocities up to 0.7 m s−1 at 40 and 74 m depth. Concurrent current profiles were measured between 0.5 and 8.5 m above the seabed at these sites and therefore the observations presented in this study allowed a detailed analysis of the wave-current interactions in the continental shelf bottom boundary layer during highly energetic tropical cyclone conditions. These observations revealed a strong modification of the current profiles during the TC with an increase of the apparent bottom roughness by up to 2 orders of magnitude compared to the typical tide-dominated current conditions. This modification was predominantly due to wave-current interactions; however, the results also suggest that changes in bed forms during the TC conditions likely acted as a secondary mechanism contributing to the enhanced bottom roughness experienced by the mean currents. A comparison of the total mean bed shear stresses as a function of the waves and currents showed a somewhat larger enhancement due to the nonlinear wave-current interactions than predicted by common semi-empirical models. Overall, the enhancement of the mean bed shear stresses during the TC significantly reduced the mean current velocities in the bottom boundary layer, highlighting the importance of including wave-current interactions within ocean circulation models to accurately predict shelf currents during TC conditions.

Our team would like to acknowledge the Bardi Jawi, the Traditional Owners both past and present, who continue to care for this country. Thanks to the Bardi Jawi Rangers and staff of the Kimberley Marine Research Station for their help and local knowledge on three field trips. We are grateful for field assistance provided by Michael Cuttler, Jordan Iles, Miela Kolomaznik, and Leonardo Ruiz-Montoya. Comments by two anonymous reviewers substantially clarified and improved earlier drafts of this paper. This work was funded by the Western Australian Marine Science Institution's Kimberley Marine Research Program (Project 2.2.3), an Australian Research Council's Future Fellowship (FT110100201) to RJL, and the ARC Centre of Excellence for Coral Reef Studies (CE140100020).

Tropical cyclones generate extreme hazards along coastlines, often leading to losses of life and property. Although coral reefs exist in cyclone‐prone regions globally, few studies have measured the hydrodynamic conditions and morphological responses of reef‐fringed coastlines to tropical cyclones. Here, we examine the impact of Tropical Cyclone Olwyn on a section of Australia's largest fringing reef (Ningaloo Reef) using in situ wave and water level observations, topographic surveys, and numerical modeling. Despite forereef significant wave heights reaching 6 m and local winds of 140 km h−1, average beach volume change was only −3 m3 m−1. The results indicate that this erosion was due to locally generated wind waves within the lagoon rather than the offshore waves that were dissipated on the reef crest. A comparison of these volume changes to observations of tropical cyclone impacts along exposed sandy beaches quantitatively demonstrates the substantial coastal protection reefs can provide against extreme storms.

The numerical wave model SWAN (Simulating WAves Nearshore) and historical wave buoy observations were used to investigate the response of surface wave fields to tropical cyclone (TC) wind forcing on the Australian North West Shelf (NWS). Analysis of historical wave data during TC events at a key location on the NWS showed that an average of 1.7 large TCs impacted the region each year, albeit with high variability in TC track, intensity and size, and also in the surface wave field response. An accurately modeled TC wind field resulted in a good prediction of the observed extreme wave conditions by SWAN. Results showed that the presence of strong background winds during a TC and a long TC lifetime (with large variations in translation speed) can provide additional energy input. This potentially enhances the generated swell waves and increases the spatial extent of the TC generated surface wave fields. For the TC translation speeds in this study, a positive relationship between TC translation speed and the resulting maximum significant wave height and wave field asymmetry was observed. Bottom friction across the wide NWS limited the amount of wave energy reaching the coastal region; consistently reducing wave energy in depths below 50 m, and in the case of the most extreme conditions, in depths up to 100 m that comprise much of the shelf. Nevertheless, whitecapping was still the dominant dissipation mechanism on the broader shelf region. Shelf-scale refraction had little effect on the amount of wave energy reaching the nearshore zone; however, refraction locally enhanced or reduced wave energy depending on the orientation of the isobaths with respect to the dominant wave direction during the TC.

The movement of water can have a significant influence on the vulnerability of hermatypic corals to environmental disturbances such as cyclone damage, heat stress and anoxia. Here, we explore the relationship between small reef-scale water circulation patterns and measured differences in the abundance, composition and vulnerability of coral assemblages over decades. Changes in coral cover and community structure within Bill’s Bay (Ningaloo Reef, Western Australia) over a 22-yr period, during which multiple disturbance events (including mass bleaching, anoxia, and tropical cyclones) have impacted the area, were compared with spatial variation in water residence times (WRT). We found that reef sites associated with longer water residence times (WRT >15 h) experienced higher rates of coral mortality during acute environmental disturbances compared to reef sites with shorter WRT. Shifts in coral community composition from acroporid to faviid-dominated assemblages were also more prominent at sites with long WRT compared to reef sites with shorter WRT, although shifts in community composition were also observed at sites close to shore. Interestingly, these same long-WRT sites also tended to have the fastest recovery rates so that coral cover was returned to original levels of approximately 20% over two decades. This study provides empirical evidence that spatial patterns in water circulation and flushing can influence the resilience of coral communities, thus identifying areas sensitive to emerging threats associated with global climate change.

Benthic dissolved oxygen fluxes were measured on the reef flat of Tallon Island, an intertidal reef platform in the Kimberley region of northwestern Australia, for periods of 2 weeks in the wet and dry seasons. This reef flat is strongly tidally forced by semidiurnal tides (spring range > 8 m) and experiences highly asymmetric water level variability, with ebb durations lasting ∼10 h; this results in diel variations in water temperature and dissolved oxygen (DO) concentration (up to ∼11°C and 440 μM, respectively) that are among the most extreme recorded for reefs worldwide. Given the consistent tidal flow patterns, a one-dimensional control volume approach was used to make continuous Eulerian measurements of net production and community respiration from observed changes in DO within two zones: an inner zone dominated by seagrass and an outer zone dominated by macroalgae. Community respiration (R) was controlled primarily by DO concentration; however, fluxes approached the limits of DO mass transfer at low flow speeds. Estimates of gross primary production (P) suggested that reef communities were able to fix carbon at rates comparable to other tropical seagrass and mixed reef flat communities despite short-term (∼hours) extremes in light (up to 1800 μmol m−2 s−1) and temperature (> 35°C). Daily net community production fluctuated between net autotrophy and heterotrophy over a ∼15 d period depending on the phase difference between the solar and tidal cycles but was nonetheless metabolically balanced on time scales greater than weeks (P : R = 1.0–1.1).

A feedback between seagrass presence, suspended sediment and benthic light can induce bistability between two ecosystem states: one where the presence of seagrass reduces suspended sediment concentrations to increase benthic light availability thereby favoring growth, and another where seagrass absence increases turbidity thereby reducing growth. This literature review identifies (1) how the environmental and seagrass meadow characteristics influence the strength and direction (stabilizing or destabilizing) of the seagrass-sediment-light feedback, and (2) how this feedback has been incorporated in ecosystem models proposed to support environmental decision making. Large, dense seagrass meadows in shallow subtidal, non-eutrophic systems, growing in sediments of mixed grain size and subject to higher velocity flows, have the greatest potential to generate bistability via the seagrass-sediment-light feedback. Conversely, seagrass meadows of low density, area and height can enhance turbulent flows that interact with the seabed, causing water clarity to decline. Using a published field experiment as a case study, we show that the seagrass-sediment-light feedback can induce bistability only if the suspended sediment has sufficient light attenuation properties. The seagrass-sediment-light feedback has been considered in very few ecosystem models. These models have the potential to identify areas where bistability occurs, which is information that can assist in spatial prioritization of conservation and restoration efforts. In areas where seagrass is present and bistability is predicted, recovery may be difficult once this seagrass is lost. Conversely, bare areas where seagrass presence is predicted (without bistability) may be better targets for seagrass restoration than bare areas where bistability is predicted.

Australia has the third-largest ocean territory on Earth, with 85% of Australians living within 50 km of the coast. As a result, coasts and ocean matter to Australia and are integral to the use of marine resources for sustainable economic development, i.e. Australia's blue economy. The societal, economic and cultural issues associated with the blue economy range from marine sovereignty, safety and security to food and energy security, biodiversity conservation, management and coastal populations. Marine, climate and Antarctic science have the potential to drive the development of Australia's blue economy through the creation of new knowledge, tools, technology, and innovation. This requires observations from the past to the present, as well as numerical modelling capability that can hindcast, nowcast, and forecast the marine environment with skill.

We report seasonal changes in coral calcification within the highly dynamic intertidal and subtidal zones of Cygnet Bay (16.5°S, 123.0°E) in the Kimberley region of northwest Australia, where the tidal range can reach nearly 8 m and the temperature of nearshore waters ranges seasonally by ~9 °C from a minimum monthly mean of ~22 °C to a maximum of over 31 °C. Corals growing within the more isolated intertidal sites experienced maximum temperatures of up to ~35 °C during spring low tides in addition to being routinely subjected to high levels of irradiance (>1500 µmol m−2 s−1) under near stagnant conditions. Mixed model analysis revealed a significant effect of tidal exposure on the growth of Acropora aspera, Dipsastraea favus, and Trachyphyllia geoffroyi (p ≤ 0.04), as well as a significant effect of season on A. aspera and T. geoffroyi (p ≤ 0.01, no effect on D. favus); however, the growth of both D. favus and T. geoffroyi appeared to be better suited to the warm summer conditions of the intertidal compared to A. aspera. Through an additional comparative study, we found that Acropora from Cygnet Bay calcified at a rate 69 % faster than a species from the same genus living in a backreef environment of a more typical tropical reef located 1200 km southwest of Cygnet Bay (0.59 ± 0.02 vs. 0.34 ± 0.02 g cm−2 yr−1 for A. muricata from Coral Bay, Ningaloo Reef; p

We examined the seasonal and spatial variability in the temperatures of nearshore reef waters over 19 months across Coral Bay at Ningaloo Reef, Western Australia. Local deviations in the mean daily temperature of nearshore reef waters from offshore values (DT) were a linear function of the combined effect of net atmospheric heating (Qnet) and offshore wave height and period Hs ffiffiffiffiffi tp p �� . Whereas intra-annual variation in local heat exchange was driven mainly by seasonal changes in shortwave radiation, intra-annual variation in local cooling was driven mostly by changes in relative humidity (r2 5 0.60) and wind speed (r2 5 0.31) that exhibited no apparent seasonality. We demonstrate good agreement between nearshore reef temperatures modeled from offshore sea surface temperatures, offshore wave forcing, and local atmospheric heat fluxes with observed temperatures using a simple linear model (r2 5 0.31–0.69, root-mean-square error 5 0.4–0.9uC). Using these modeled nearshore reef temperature records, we show that thermal stresses across the reef reached between 16uC weeks and 22uC weeks in the summer of 2011 when a mass coral bleaching event was reported, and between 12uC weeks and 13uC weeks in the following summer of 2012 when no mass bleaching was reported. After compensating for differences between observed and modeled thermal stresses, we found that maximum thermal stresses across the reef likely reached as high as 18–34uC weeks in the summer of 2011. The approach used here could thus improve our ability to predict spatial variation in thermal stress and bleaching across other wavedriven nearshore reef systems.

The dynamics of the summer circulation in the coastal waters off Perth in Western Australia were investigated during a two-month field experiment. The study included the deployment of an array of moorings spanning the outer shelf, the inner shelf, within the inshore Perth coastal lagoon, and in the large coastal embayment of Cockburn Sound. The results revealed highly transient coastal circulation patterns that responded to variability in both the locally- and remotely-generated forcing. Local wind forcing played a primary role in driving much of the alongshore current variability at the shallower (

Hydrodynamic data (time series of tidal velocities and vertical stratification) were collected during the winter of 2009 in Shark Bay, Western Australia, to document water exchange between the bay and the ocean. The net loss of freshwater through evaporation causes salinity levels in Shark Bay to be higher than the adjacent ocean, leading to its classification as an inverse estuary. The observations revealed pulses of near-bed dense water outflows (velocity ∼0.10 m s −1 ) at weekly to fortnightly intervals, associated with periods of turbulent mixing when tidal velocities and winds were both weak. Although tidal mixing appeared to be the main control on the formation of the outflows, wind mixing during strong wind events was also sufficient to destratify the water column and interrupt the density-driven circulation. These data represent the first direct measurements of exchange flows in the entrance channels of Shark Bay and reveal a mechanism to maintain the balance of salinity as well as contribute to the exchange of material (e.g., larvae) between the bay and the ocean.

We examined spatial and temporal variations in particulate organic matter (POM) dynamics over a fringing coral reef (Ningaloo Reef) in Western Australia during the austral autumn and spring. Total POM concentrations generally did not differ between seasons or reef zones, but the composition of POM, in terms of carbon isotope ratios (δ13C-POM), carbon to nitrogen ratios (C: N), and fatty acids, changed consistently in water flowing across the reef. Both δ13C-POM and C: N increased from the fore reef to the reef flat and lagoon, −23.0‰ to −20.1‰ and 7.31 to 8.34, respectively. Average rates of net POM uptake by the reef community were highest over the reef crest (4 to 30 mmol N m-2 d-1 and 6 to 130 mmol C m-2 d-1), with a Bayesian isotope model confirming independent measurements of high uptake rates of allochthonous POM (oceanic phyto-and zooplankton). In contrast, over the reef flat, net release of POM was observed (-4 to -5 mmol N m-2 d-1 and -50 mmol C m-2 d-1), with gross release rates (estimated as -6 to -8 mmol N m-2 d-1 and -30 to -90 mmol C m-2 d-1) indicating that the release of autochthonous POM may be of similar magnitude to allochthonous uptake. Examining POM dynamics in terms of gross fluxes reinforces the dependence of coral reef systems on oceanographic processes for allochthonous POM supply, as well as highlighting the potential for autochthonous POM production to supply nutrients to benthic and pelagic communities downstream.

Two widely distributed seagrasses in Western Australia with contrasting dispersal strategies were studied in terms of their physical characteristics and morphology to understand how physical processes (wind, waves, and currents) drive dispersal. Posidonia australis releases floating fruit that contain a single negatively buoyant seed that lacks dormancy. Halophila ovalis produces fruit and dormant seeds that sit on the sediment surface. The floating stage of P. australis was assessed in situ by tracking the movement of the fruit directly on the ocean surface, together with drifter devices to differentiate between the transport induced by surface currents and wind. The dehiscence time of P. australis fruit was evaluated in seawater tanks, and the associated viability of the seeds was assessed by growth after dehiscence. The settling velocities of P. australis seeds and H. ovalis fruit and seeds were quantified in settling tubes with image-processing techniques to track the fall trajectories. The re-suspension thresholds of the seeds were calculated based on the critical bed shear stresses required to transport the seeds in a unidirectional flow flume. P. australis can travel long distances at the air-sea interface (∼ 55 km), due to wind alone, during its floating stage. The settling velocities of P. australis and H. ovalis seeds (ws = 10.6 ± 0.4 cm s−1 and 4.7 ± 0.1 cm s−1, respectively) and their re-suspension thresholds (τ = 107 ± 4 mPa and 66 ± 1 mPa, respectively) suggest that secondary movement is restricted, but likely to be produced by stronger wave-induced shear stress events.

Nitrate and nitrite (NO x) and phosphate (PO 4) dynamics over Ningaloo Reef, Western Australia, are shown to depend on oceanographic forcing of coupled mass transfer limited (MTL) gross uptake and gross release from remineralized oceanic particulate organic matter (POM). Estimates of gross release rates increased significantly with increasing POM uptake and were of the same order as gross uptake rates. Gross uptake rates increased significantly with increasing oceanic concentrations and wave energy dissipation, were 35-80 higher over the reef crest (7-9 mmol NO x m -2 d -1 and 4-5 mmol PO 4 m -2 d -1), and were significantly correlated with independent estimates of POM-mediated gross NO x uptake, supporting both MTL uptake and the strong role of oceanic POM supply. The relative supply of NO x and POM was linked to the seasonal dynamics of a regional current system. In late spring, upwelling associated with seasonally strong equator-ward winds led to increased NOx concentrations (0.71 ± 0.2 I¼mol L -1), POM NO x and the reef was a net nutrient source (-7060 mmol NO x m -1 d -1 and -730 mmol PO 4 m -1 d -1). The autumn enhancement of oceanic POM supply to the reef can be attributed to a regional phytoplankton bloom associated with acceleration of the oligotrophic Leeuwin Current, which may result in a significant supply of dissolved nutrients to downstream communities. © 2012, by the Association for the Sciences of Limnology and Oceanography, Inc.

Rates of net community carbon production (mmol C m−2 h−1) were measured continuously in an algal-dominated reef flat community on the Kaneohe Bay barrier reef, Hawaii, for 12 days at the end of October 2006. The weather became increasingly cloudy during the last 5 days of measurements, resulting in a sevenfold decline in daily incident light (28–4 Ein m−2 d−1). In response, gross primary production (P) for the reef flat community also decreased sevenfold, varying linearly with light (r2 = 0.92, n = 12). Community respiration (R) decreased fivefold over this same period and was highly correlated with changes in P (r2 = 0.84, n = 12). We reason that this short-term coherence between P and R indicates that most of the carbon fixed during this period was rapidly metabolized via plant respiration. We further conclude that the dominance of autotrophic respiration under general conditions of nutrient-limited growth can explain much of the balance between P and R that is commonly observed in shallow reef communities.

Seasonal observations of phytoplankton uptake at Ningaloo Reef, Western Australia, reinforce the importance of particulate organic nitrogen (PON) and carbon (POC) in reef nutrient budgets and identify wave action and the dynamics of regional currents (over a range of temporal and spatial scales) as important factors determining plankton supply to the reef. Phytoplankton uptake rates, calculated from declining chlorophyll a concentrations as water moved over the reef, appeared to be near the physical limits of mass transfer. Phytoplankton-derived PON flux of 2 to 5 mmol N m -2 d -1 was on the order of that typical for dissolved N uptake — confirming that particle feeding may supply the N missing in reef N budgets — while POC flux of 14 to 27 mmol C m -2 d -1 was on the order of net community metabolism. Phytoplankton supply was highly variable at daily-to- seasonal time scales in response to the dynamics of a regional current system dominated by the downwelling-favourable Leeuwin Current (LC). Acceleration of the LC in the austral autumn may supply as much phytoplankton to the reef as sporadic upwelling associated with the Ningaloo Cur- rent (NC) in summer. The ocean catchment concept is introduced as a basis for examining the spatial scale of pelagic processes influencing benthic systems: every day, Ningaloo may completely consume the phytoplankton over 87 km 2 of LC water, compared to only 20 km 2 of NC water. Production within this catchment appears insufficient to maintain offshore phytoplankton concentrations, and advec- tion of remotely sourced production into the catchment is required to balance reef uptake. A func- tional dependence by reef organisms on externally sourced ocean productivity increases the poten- tial scale at which human- or climatically induced changes may affect reef communities and suggests that processes such as changes in offshore currents and plankton communities require further con- sideration in reef-level biogeochemistry.

Surf zone drifters and a current meter were used to study the nearshore circulation patterns in the lee of groynes at Cottesloe Beach and City Beach in Western Australia. The circulation patterns revealed that a persistent re-circulation cell was present in the lee of the groyne which was driven by changes in wave set-up resulting from lower wave heights in the lee of the groyne. The re-circulation consisted of a longshore current directed towards the groyne which was deflected offshore due to groyne resulting in a rip current along the groyne face. The offshore-flowing rip current and the incoming waves converged at the offshore extent of this circulation cell, with the deflection of the rip current parallel to the shoreline and then completing the recirculation through an onshore component. The Eulerian measurements revealed that 55% of the currents on the lee side of the groyne were directed offshore and that these currents had a maximum speed of 2 m s −1 . Spectral analysis of the wave heights and the currents revealed several corresponding peaks in the measured spectral densities with timescales between 12 s and 50 min. Numerical simulations of an idealised beach with a shore-normal groyne were conducted using a circulation model driven by waves, and confirmed the formation of a persistent eddy in the lee of the groyne. Sensitivity studies indicated that the incident wave angle, wave period, and especially the wave height controlled the circulation. The eddy vorticity, a measure of an eddy's strength, increased roughly proportional to an increase in the incident wave energy flux.

Both canopy flow and porous media theories have been developed independent of one another to predict flow through submerged porous structures. These approaches are very similar, albeit with some key differences in how canopy resistance forces are parameterized. Canopy models provide a means of parameterizing the shear stresses that occur at the top of the canopy, whereas porous media models can often provide a simpler and more tractable way of parameterizing turbulent form drag based on simple morphological metrics and empirical relationships already in the hydrology literature. We developed a set of equations combining aspects of both models and applied this hybridized model to predict the flow structure within an experimental canopy formed by the branching coral Porites compressa, using model parameter values obtained from the literature. Results from the model predictions agreed well with direct measurements of flow speed and flow forces derived from particle image velocimetry under conditions of both unidirectional and wave-driven oscillatory flow.

A field program was implemented on a fringing reef located on Oahu, Hawaii, to investigate the dispersion characteristics of near-bed dye plumes, tracked using an autonomous underwater vehicle (AUV) with an onboard fluorometer. The combination of moored and AUV-based measurements collected synchronously in this study allowed us not only to observe the dispersion characteristics of individual plumes, but importantly to isolate the flow structures directly responsible for dispersion under a variety of forcing conditions. The evolution of several plumes was observed, each influenced by different wave (surface and internal), current, and stratification conditions. The observed dispersion was caused by both turbulent dispersion and plume meandering. Lateral turbulent dispersion coefficients were roughly an order of magnitude greater than previous observations on sandy beach sites, which is likely attributable to the enhanced surface wave-induced mixing and the large physical roughness of the reef. For a large portion of the 2-week experiment the effects of meandering dominated over turbulent dispersion (on average 1.5 times greater). The meandering was the result of large-scale cross-reef current variability. Moored thermistor chain data on the forereef suggest that the source of this cross-reef flow variability were packets of solitary waves that accompanied the propagation of baroclinic bores up the reef slope. Baroclinic bores dissipated before they reached the inner reef when surface wave conditions were large, resulting in the reduction of plume meandering during this period.

We examined the importance of nonlocal turbulence to the mass transfer of dissolved species from both cylinders and models of reef coral. Solid gypsum cylinders and gypsum-coated model coral were dissolved in an outdoor flume at mean flow speeds of 4.5 and 10 cm s21. Three model corals were used: two branched forms of the genera Acropora and Pocillopora, and one lobate form of the genus Platygyra. Turbulence intensities (Tu) were measured as the ratio of the standard deviation of the time-variant flow to the mean. Tu of between 5% and 55% were created independently of the mean flow by pumping water through two vertical arrays of jets. Mass transfer coefficients increased by 10–70% with turbulence intensity for all forms at both mean flow speeds considered (p , 0.05); however, mass transfer coefficients for the branched coral were not as sensitive to changes in turbulence intensity as for the lobate coral. Results for the cylinders were consistent with the engineering literature and indicate that the effects of turbulence intensity on mass transfer become weaker when branch size or flow speed (or both) become very small. Turbulence intensities measured around experimental coral communities and above naturally occurring reef communities typically vary between 15% and 35%. Assuming an average turbulence intensity of around 25%, then ignoring the effects of nonlocal turbulence altogether would resul ti n uncertainties in mass transfer coefficients of at most 610% for the lobate coral form and 65% for the branched coral forms. Measuring external turbulence in bulk flows is not necessary for most evaluations of biogeochemical rates in benthic reef systems.

We describe a laboratory investigation into the effect of turbulent hydrodynamic stresses on clam larvae in the settlement phase of the recruitment process. A two-component laser-Doppler anemometer (LDA) was used to measure time histories of the instantaneous turbulence structure at potential recruitment sites within reconstructed beds of the adult Asian clam, Potamocorbula amurensis.Measurements were made for two flow speeds over beds with three different clam densities and two different clam heights. We analyze the statistical effect of the turbulence on the larval flux to the bed and on the probability of successful anchoring to the substrate. It is shown that the anchoring probability depends on the nature of the instantaneous stress events rather than on mean stresses. The instantaneous turbulence structure near the bed is altered by the flow rate and the spacing and height of adult clams living in the substrate. The ability to anchor quickly is therefore extremely important, since the time sequence of episodic turbulent stress events influences larval settlement success. The probability of successful larval settlement is predicted to decrease as the spacing between adults decreases, implying that the hydrodynamics impose negative feedback on clam bed aggregation dynamics. Species success, population density, and community structure are all dependent on larval recruitment. Therefore, the processes of settlement and recruitment of benthic and epibenthic communities have been the subject of substantial research (see Olafsson et al. 1994; Wildish and Kristmanson 1997 for recent reviews). A major portion of the work has involved the transport of larvae to the bed and settling of the larvae by passive or active selection processes ( see reviews by Butman 1987; Abelson and Denny 1997). Several researchers have found that it is the combination of larval behavior (e.g., swimming, crawling, burrowing) and physical processes that deliver the larvae to the bed that is responsible for the recruitment success (Mullineaux and Butman 1990; Butman and Grassle 1992; Grassle et al. 1992; Snelgrove et al. 1993). As summarized by Underwood and Keough (2001), it is no longer a question of whether hydrodynamics or behavior are important in recruitment, rather it is a question of ‘‘under which conditions is larval behavior important?’’ We will expand this question and say that it is also important to determine the periods, during the relevant physical processes, when larval behavior is important. Related to the interest in larval recruitment is an ecological interest in what regulates temporal, spatial, and agesegregated distributions of species. Thus, the processes important in determining how aggregations of benthic 1

Four boat-based surveys and several moored measurements were conducted over the dry season in June, July, August and September 2008 in the central Kimberley region of northwestern Australia; a macrotidal tropical coastal region, characterised by numerous island archipelagos and shallow reefs. The objective was to determine the influence of this complex morphology on the biophysical properties of the local coastal water masses and the resultant impact on phytoplankton biomass. Despite negligible rainfall during the dry-season, decreased salinity towards the coast suggested a persistent fresh water source. The water column was weakly vertically-stratified throughout much of the study region, only becoming well-mixed in topographically constricted regions. The vertical stratification resulted in a cross-shore subsurface in situ chl- a fluorescence maxima (at ∼30 m depth) in June, July and August. The presence of a chain of islands and shallow reefs led to the partial isolation of the semi-enclosed embayment, Collier Bay, creating distinct water masses across this relatively small area. The confluence of the two most distinct water masses formed a front at latitude ∼15.65–15.7 °S, in both June and August, indicating it was a persistent feature during the dry season. In situ chl- a fluorescence was highest at the front location. In Collier Bay, NO x concentrations were up to five times higher, with a 20% higher proportion of larger extracted chl- a biomass (cells > 5 μm), a proxy for phytoplankton. In the more open waters of Camden Sound, relatively high concentrations of picophytoplankton, bacteria and viruses were observed. Such spatial shifts in nutrient concentrations, phytoplankton biomass and phytoplankton and microbial community composition across the persistent density front are likely to have important consequences on the region's planktonic food web function.

A 3 week field study was conducted to investigate the dynamics of low-frequency (infragravity) wave motions over a fringing reef at Ningaloo Reef, Western Australia. Short-period wave motions (0.04–0.2 Hz) were observed to dissipate on the reef crest beyond which infragravity wave motions (0.004–0.04 Hz) gradually dominated toward the lagoon. However, both the short waves and the infragravity waves were relatively small (both

Rates of net production, net calcification, and nutrient uptake were measured in a coral-dominated reef flat community on Ningaloo Reef in northwestern Australia under seasonally minimum and maximum light levels. Daily integrated light decreased twofold while water temperatures remained relatively constant increasing by only 1°C on average from summer to winter. Rates of daily community gross primary production (GPP) were only 33% ± 9% higher in summer than in winter (1400 ± 70 versus 1050 ± 60 mmol C m−2 d−1), far less than the twofold seasonal changes reported for most shallow reef communities. Rates of daily community net calcification (Gnet) were not significantly different between seasons (190 ± 40 mmol CaCO3 m−2 d−1 in summer versus 200 ± 10 mmol CaCO3 m−2 d−1 in winter). The average rate of total nitrogen uptake (dissolved + particulate) was also not significantly different between summer and winter (8.3 ± 3.8 versus 6.6 ± 3.4 mmol N m−2 d−1, respectively), despite evidence of sporadically high nitrate uptake in both seasons. In summer, rates of hourly net calcification (gnet) were linearly correlated with diurnal changes in net production, pH, and aragonite saturation state (Ωar); and were mostly correlated with light except at mid-day under heavy cloud cover. However, in winter,gnet was independent of diurnal changes in light, net production, pH, and Ωar indicating that the reef flat community had possibly reached a threshold above which rates of net calcification were insensitive to diurnal changes in their environment.

[1] We investigated the influence of hydrodynamic forcing (waves, tides, alongshore currents and winds) and net calcification by coral reef organisms on the spatial distribution of total alkalinity (TA) in a fringing reef system through a combination of field measurements and numerical modeling. A field experiment was conducted over 10 days in Coral Bay (Ningaloo Reef, Western Australia) during which we measured wave heights, currents, and tides as well as the spatial distribution of TA across the fore reef, reef crest, and lagoon. We used observed changes in TA on the adjacent reef flat, along with synoptic measurements of cross-reef transport, to estimate in situ rates of net calcification (gcv) using a control volume approach. Based on the gcv estimated, we simulated light-driven, diurnal variations in benthic net calcification within a three-dimensional ocean circulation model, ROMS (Regional Ocean Modeling System). By coupling ROMS with a spectral wave model (Simulating Waves Nearshore), we were able to simulate currents within Coral Bay reef-lagoon system that were in good agreement with the field observations and demonstrate that circulation with the system was wave-dominated. Both the field measurements and numerical model output confirmed that both residence time (τR) and TA varied primarily with offshore wave heights and location within the bay. However, variations in TA were also affected by the nonlinear interaction between rates of net calcification that varied as a function of diurnally changing light and water residence time that varied as a function of offshore wave heights.

[1] The circulation and temperature variability on the inner shelf near the North West Cape of Australia off Ningaloo Reef was investigated using field data obtained from two moorings deployed from 2004 to 2009. The results revealed that alongshore currents on the inner shelf were, on average, only weakly influenced by the offshore poleward (southward) Leeuwin Current flow, i.e., monthly averaged alongshore current velocities were ∼0.1 m s−1 or less. The presence of a consistent summer-time wind-driven equatorward (northward) counter flow on the inner-shelf (referred to in the literature as the Ningaloo Current) was not observed. Instead, the shelf waters were strongly influenced year-round by episodic subtidal current fluctuations (time scale 1–2 weeks) that were driven by local wind-forcing. Analysis of the current profiles showed that periods of strong equatorward winds were able to overcome the dominant poleward pressure gradient in the region, leading to upwelling on the inner-shelf. Contrary to prior belief, these events were not limited to summer periods. The forcing provided by these periodic wind events and the associated alongshore flows can explain much of the observed temperature variability (with timescales < 1 month) that influences Ningaloo Reef.

We examined the importance of picoplankton and virioplankton to reef trophodynamics at Ningaloo Reef, (north-western Australia), in May and November 2008. Picophytoplankton (Prochlorococcus, Synechococcus and picoeukaryotes), bacterioplankton (inclusive of bacteria and Archaea), virioplankton and chlorophyll a (Chl a) were measured at five stations following the consistent wave-driven unidirectional mean flow path of seawater across the reef and into the lagoon. Prochlorococcus, Synechococcus, picoeukaryotes and bacterioplankton were depleted to similar levels (~40% on average) over the fore reef, reef crest and reef flat (=‘active reef’), with negligible uptake occurring over the sandy bottom lagoon. Depletion of virioplankton also occurred but to more variable levels. Highest uptake rates, m, of picoplankton occurred over the reef crest, while uptake coefficients, S (independent of cell concentration), were similarly scaled over the reef zones, indicating no preferential uptake of any one group. Collectively, picophytoplankton, bacterioplankton and virioplankton accounted for the uptake of 29 mmol C m−2 day−1, with Synechococcus contributing the highest proportion of the removed C. Picoplankton and virioplankton accounted for 1–5 mmol N m−2 day−1 of the removed N, with bacterioplankton estimated to be a highly rich source of N. Results indicate the importance of ocean–reef interactions and the dependence of certain reef organisms on picoplanktonic supply for reef-level biogeochemistry processes.

[1] The role of waves, tide, and wind on the circulation of a fringing reef system was investigated using data collected during a 6 week field experiment in a section of Ningaloo Reef off Western Australia. The high correlation observed between current velocities and wave height throughout the system revealed the dominant role wave breaking plays in driving the overall reef-lagoon circulation, whereas the modulation of the currents at tidal frequencies suggested that the wave-driven currents responded to tidal variations in the mean water level over the reef. The influence of the various forcing mechanisms on the current field was investigated for both high- and low-frequency bands. Wave breaking was found to be the dominant forcing mechanism for the low-frequency (subtidal) currents, with the subtidal flow pattern consisting of a cross-reef flow over the reef, alongshore flow in the lagoon, and water exiting back to the ocean through the main channel. The tides controlled the high-frequency current variability via two mechanisms: one associated with the ebb-flood cycle of the tides and the second associated with tidal modulations of the wave-driven currents. Wind-forcing and buoyancy effects were both found to be negligible in driving the circulation and flushing of the system during the observation period. Flushing time scale estimates varied from as low as 2 h to more than a day for the wide range of observed incident wave heights. The results suggest that the circulation of Ningaloo Reef will be strongly influenced by even a small mean sea level rise.

[1] The response of the wave‐driven circulation within coastally bounded reef‐lagoon systems to varying lagoon and channel morphology was investigated using a two‐ dimensional coupled wave‐circulation numerical model. Numerical experiments were conducted using a series of coastal reefs that incorporated a wide range of different lagoon depths and channel widths. With the morphology of both the reef (forereef and reef flat) and incident wave forcing held constant, the wave‐driven circulation was found to increase substantially as dimensionless reef morphology parameters characterizing the relative lagoon depth and channel width were each independently increased. Analysis of the wave setup fields revealed that this increased flow was due to an enhancement of the cross‐reef water level gradient, resulting from a sharp reduction in the lagoon setup as the frictional resistance on the lagoon‐channel return flow was diminished. This follows similar trends observed in existing field and laboratory studies of wave‐driven reef flows. Analysis of flushing time scales computed for each reef‐lagoon geometry predicted the existence of optimal dimensionless lagoon depths and channel widths for a reef system, to establish maximal coastal flushing. Overall, the circulation and flushing of coastal reef‐lagoon systems was found to be largely controlled by the particular morphology of the lagoon and channel region rather than solely by the morphology of the forereef and reef flat that has been the primary focus of analytical models developed to predict wave setup and circulation on reefs.

[1] A coupled wave-circulation numerical model was used to simulate the distribution of wave energy, as well as the circulation induced by wave breaking, wind, and tidal forcing, within a coral reef system in Kaneohe Bay, Oahu, Hawaii. Modeled wave, current, and wave setup fields were compared with field measurements collected on the forereef, reef flat, and reef channels and in the lagoon over a 4-week period. The predicted wave height transformation across the reef-lagoon system was in good agreement with field observations, using single-parameter (spatially uniform) values to describe both wave-breaking and frictional dissipation. The spatial distribution of the resulting wave setup field drove a persistent wave-driven flow across the reef flat that returned to the ocean through two deeper channels in the reef. Both the magnitude and direction of these currents were well described using a spatially uniform hydraulic roughness length scale. Notably, the model lends support to field observations that setup within the coastally bounded lagoon was a substantial fraction of the maximum setup on the reef (∼60–80%), which generated relatively weak cross-reef wave-driven flows (∼10–20 cm s−1) compared with reefs having mostly unbounded lagoons (e.g., many atolls and barrier reefs). Numerical experiments conducted using Lagrangian particle tracking revealed that residence times within Kaneohe Bay are extremely heterogeneous, typically ranging from 1 month within its sheltered southern lagoon.

[1] Communities of benthic organisms can form very rough surfaces (canopies) on the seafloor. Previous studies have shown that an oscillatory flow induced by monochromatic surface waves will drive more flow inside a canopy than a comparable unidirectional current. This paper builds on these previous studies by investigating how wave energy is attenuated within canopies under spectral wave conditions, or random wave fields defined by many frequencies. A theoretical model is first developed to predict how flow attenuation within a canopy varies among the different wave components and predicts that shorter-period components will generally be more effective at driving flow within a canopy than longer-period components. To investigate the model performance, a field experiment was conducted on a shallow reef flat in which flow was measured both inside and above a model canopy array. Results confirm that longer-period components in the spectrum are significantly more attenuated than shorter-period components, in good agreement with the model prediction. This paper concludes by showing that the rate at which wave energy is dissipated by a canopy is closely linked to the flow structure within the canopy. Under spectral wave conditions, wave energy within a model canopy array is dissipated at a greater rate among the shorter-period wave components. These observations are consistent with previous observations of how wave energy is dissipated by the bottom roughness of a coral reef.

[1] Mass transfer rates from submerged canopies constructed from arrays of vertical cylinders were investigated for a range of different cylinder spacings under both unidirectional and oscillatory flow. Individual canopy elements made from gypsum were dissolved in fresh water to simulate the mass transfer of dissolved metabolites to and from canopies of living benthic organisms. Mass transfer rates under oscillatory flow were up to three times higher than values measured for a comparable unidirectional current. This enhancement was shown to be a strong function of the canopy element spacing. A model was developed to predict canopy mass transfer rates on the basis of the in-canopy flow speed and was generalized to incorporate either unidirectional or oscillatory flow. Agreement between the modeled and experimentally measured mass transfer rates indicate that enhanced mass transfer to/from living benthic canopies under oscillatory flow is driven primarily by the higher in-canopy water motion generated by the oscillatory flow, as detailed in the companion paper (Lowe et al., 2005).

[1] Many benthic organisms form very rough surfaces on the seafloor that can be described as submerged canopies. Recent evidence has shown that, compared with a unidirectional current, an oscillatory flow driven by surface waves can significantly enhance biological processes such as nutrient uptake. However, to date, the physical mechanisms responsible for this enhancement have not been established. This paper presents a theoretical model to estimate flow inside a submerged canopy driven by oscillatory flow. To reduce the complexity of natural canopies, an idealized canopy consisting of an array of vertical cylinders is used. The attenuation of the in-canopy oscillatory flow is shown to be governed by three dimensionless parameters defined on the basis of canopy geometry and flow parameters. The model predicts that an oscillatory flow will always generate a higher in-canopy flow when compared to a unidirectional current of the same magnitude, and specifically that the attenuation will monotonically increase as the wave orbital excursion length is increased. A series of laboratory experiments are conducted for a range of different unidirectional and oscillatory flow conditions, and the results confirm that oscillatory flow increases water motion inside a canopy. It is hypothesized that this higher in-canopy flow will enhance rates of mass transfer from the canopy elements, a problem formally investigated in a companion paper (Lowe et al., 2005b).

[1] A 2 week field experiment was conducted to measure surface wave dissipation on a barrier reef at Kaneohe Bay, Oahu, Hawaii. Wave heights and velocities were measured at several locations on the fore reef and the reef flat, which were used to estimate rates of dissipation by wave breaking and bottom friction. Dissipation on the reef flat was found to be dominated by friction at rates that are significantly larger than those typically observed at sandy beach sites. This is attributed to the rough surface generated by the reef organisms, which makes the reef highly efficient at dissipating energy by bottom friction. Results were compared to a spectral wave friction model, which showed that the variation in frictional dissipation among the different frequency components could be described using a single hydraulic roughness length scale. Surveys of the bottom roughness conducted on the reef flat showed that this hydraulic roughness length was comparable to the physical roughness measured at this site. On the fore reef, dissipation was due to the combined effect of frictional dissipation and wave breaking. However, in this region the magnitude of dissipation by bottom friction was comparable to wave breaking, despite the existence of a well-defined surf zone there. Under typical wave conditions the bulk of the total wave energy incident on Kaneohe Bay is dissipated by bottom friction, not wave breaking, as is often assumed for sandy beach sites and other coral reefs.