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Accurate prediction of coastal flooding requires a detailed understanding of all individual contributions to sea level variability and how they interact to trigger extreme sea level (ESL) events. In this study, we focus on the expansive (∼10,000 km) coastline of Western Australia, a region that experiences large latitudinal gradients in met‐ocean sources of sea level variability, as a case study to investigate the mechanisms responsible for ESLs and trends over the past 54 years (1966–2019). Using long‐term sea level records from tide gauges and satellite altimetry, we explore how different contributions to sea level variability at different time scales (from hourly to interannual) interact to generate ESLs. We observe that all individual, nontidal contributions to ESLs (i.e., atmospheric surge, seasonal and interannual variability) are of similar magnitude (of order 10 cm) along the entire coast and comparable to the tidal variations in the microtidal southwestern region. The results reveal the important role that seasonal and interannual sea level variability plays in generating ESLs, with these low‐frequency contributions being relatively large compared to typical global values. With mean sea level having risen by ∼10 cm over this 54‐year study period, sea level rise was also identified as making an increasingly significant contribution to observed increases in the frequency of ESLs. Overall, due to the comparatively large magnitude of low‐frequency sea level contributions (seasonal and longer), the Western Australia coast provides a useful case study to investigate how sustained periods of elevated sea level will impact coastlines worldwide more broadly in the future.

The physical roughness (canopies) formed by organisms within aquatic ecosystems (e.g., seagrass, kelp, and mangroves) modifies the local wave-driven hydrodynamics within coastal and estuarine regions. In wave-dominated environments, an understanding of the mean wave-driven flows generated within and above canopies is important, as it governs material transport (e.g., of nutrients, sediment, and biota). However, until recently the effect of submerged canopies on wave-current interactions and the resulting mean (wave-averaged) flow dynamics has received relatively little attention. In this study, a combination of wave flume experiments and numerical modeling is used to investigate the wave-induced mean flow profiles in the presence of a submerged canopy. The measured velocities and vegetation forces were used to derive bulk drag and inertia coefficients, and to validate a nonhydrostatic 2DV wave-flow model. The numerical model results were used to conduct an in-depth analysis of the mean horizontal momentum terms responsible for driving the mean (horizontal) flow within and above the submerged canopies. We show that the mean canopy hydrodynamics are driven by vertical gradients in wave and turbulent Reynolds stresses, balanced by the mean canopy drag forces. The wave Reynolds stress gradient is the dominant force driving the in-canopy mean flow and is directly related to the vorticity that is generated when the wave orbital motions become rotational near the canopy interface. This study provides new insight in the mechanisms responsible for wave-driven mean flows within submerged canopies and guidance for how these hydrodynamics can be predicted in coastal wave-circulation models.

Shear stresses on vegetated beds play an important role in driving a wide range of processes at the sediment-water interface, including sediment transport. Existing methods for the estimation of bed shear stress are not applicable to vegetated beds due to the significant alteration of the near-bed velocity profile and turbulence intensities by the vegetation. In addition, bed shear stress distributions are highly spatially variable in the presence of vegetation. In this study, computational fluid dynamics simulations were used to investigate the spatial variability of bed shear stresses in the presence of emergent vegetation (modeled as arrays of circular cylinders) and the variation of bed stress with characteristics of both the bulk flow and the array. A recently proposed model that assumes a linear variation of stress in the viscous layer immediately above the bed is shown to be a reliable tool for estimating the spatially averaged bed shear stress over a wide range of flow conditions and vegetation densities. However, application of this model is found to be restrictive due to the lack of a reliable predictive tool for the thickness of the viscous layer. Based on a balance between turbulent kinetic energy production in the vegetation stem wakes and the viscous dissipation of turbulent kinetic energy at the bed, an enhanced formulation is proposed to predict the thickness of the viscous layer, which significantly improves the accuracy of model predictions. This improved model enhances the predictive capability for important benthic processes (such as sediment transport) in vegetated aquatic systems.

Owing to their strong forcing of the ocean surface, tropical cyclones strongly modify the hydrodynamics of Australia's North West Shelf (one of the world's tropical cyclone hotspots), which in turn plays a dominant role in its sediment dynamics. Previous modeling studies have focused on describing the short term sediment dynamics during individual tropical cyclones, but have lacked validation of the responses using field observations. As a consequence, the long term cumulative impact of the tropical cyclones on the residual sediment transport pathways at the shelf scale remains unclear. In this study we apply a sediment transport model over the North West Shelf, validate its performance using an extensive field dataset, and implement a 14 year‐long model simulation to assess the sediment fluxes. The model results confirm the overwhelming role tropical cyclones play on sediment transport processes over most of the shelf, despite each cyclone only influencing a small portion of the shelf at a particular time. Overall we identified 19 tropical cyclone events over the 14 year period, which despite accounting for less than 5% of time, were found to drive the majority of both the suspended sediment alongshore and seaward cross‐shore transport. The results revealed significant inter‐annual variability of the tropical cyclone‐induced sediment dynamics with greater suspended transport during the 3 consecutive Ningaloo Niño years (2011‐2013) where sea surface temperatures off northwestern Australia were anomalously warm with elevated tropical cyclone activity.

Over a three year period, two marine heat waves occurred along the coast of Western Australia (WA) during the alternate austral summer periods of 2010/11 and 2012/13, both linked to the strong La Nina conditions. This led to severe impacts to marine ecosystems over more than 12 degrees of latitude, including unprecedented bleaching of many coral reefs, with sea surface temperature (SST) anomalies reaching up to 5 o C above climatological averages. However, despite occurring during similar climate (La Nina), the observed warming patterns differed substantially between the two heat waves, with the central coast of WA (south of 22 o S) experiencing its greatest warming in 2010/11; whereas, the northwestern coast (north of 22 o S) experiencing higher warming in 2012/13. To investigate how oceanic and atmospheric processes drove these very different spatial patterns, we conducted an ocean heat budget analysis of the region using a combination of remote sensing observation, in situ data, and a high resolution (~1 km) numerical ocean model (Regional Ocean Modeling System). The results revealed a substantial spatial differences in the contributions made by along-shelf heat advection and air-sea heat exchange between the two heat wave events. During 2010/11, anomalous heat advection was present across the entire region, but was much stronger south of 22 o S where the poleward flowing Leeuwin Current consolidates. During 2012/13, air-sea heat exchange had a much more positive (warming) influence on the SSTs (especially in the northwest), and when combined with the more positive contribution also made by heat advection north of 22 o S, can explain the regional differences in warming between the two events. Overall, the results highlight how subtle differences in regional oceanic and atmospheric heat fluxes can lead to regional heterogeneity in warming patterns during marine heat waves, even when under the influence of similar large-scale climate drivers.

Rocky reef coastlines typically feature highly variable and often abrupt cross-shore and alongshore changes in bathymetry. The effects of this irregular rocky bathymetry on the dynamics of infragravity waves are largely unknown. Most models of infragravity wave dynamics have been developed and validated on smooth alongshore-uniform bathymetries, which may break down over these highly variable bathymetries. A 2 week field experiment was conducted on a rocky reef-fringed beach to investigate how the variable bathymetry affects the spatial and temporal variability of infragravity waves. The height of short (sea-swell) waves decreased over the shallow reef due to breaking, whereas the height of infragravity waves increased toward the shoreline. Both during a storm event (Hm0 = 2.3 m) and under moderate wave conditions (Hm0 = 1.0–1.8 m), the infragravity waves formed a persistent cross-shore standing wave pattern along the entire shoreline, despite the irregular bathymetry. In addition, the alongshore components of infragravity waves refracted by the presence of the nearshore reef were observed to propagate in opposite directions up and down the coast resulting in a local alongshore standing wave pattern. Thus, the presence of highly variable nearshore bathymetry, which commonly occurs along rocky reef coastlines, may produce both cross-shore and alongshore standing wave patterns.

Funding support for this research was provided by an ARC Laureate Fellowship (LF120100049) awarded to M.M., the ARC Centre of Excellence for Coral Reef Studies (CE140100020), and the Gorgon Barrow Island Net Conservation Benefits Fund as part of the Pilbara Marine Conservation Partnership. We would like to thank Kai Rankenburg from the Advanced Geochemical Facility for Indian Ocean Research (UWA) for his technical support and assistance for the geochemical analysis of the coral samples. We also thank Ron Kanters from Bulk-Bill X-Ray, Forrestfield, Western Australia, for providing X-rays of the coral slices used for this research project. The data supporting the analysis and conclusions can be found in Supporting Information.

The influence of vegetation canopies on the flow structure in streams, rivers, and floodplains is heavily dependent on the cumulative drag forces exerted by the vegetation. The drag coefficients of vegetation elements within a canopy have been shown to be significantly different from the well-established value for a single element in isolation. This study investigates the mechanisms that determine canopy flow resistance and proposes a new model for predicting canopy drag coefficients. Large Eddy Simulations were used to investigate the fine-scale hydrodynamics within emergent canopies with solid area fractions ( λ) ranging from 0.016 to 0.25. The influences of three mechanisms in modifying canopy drag, namely, blockage, sheltering, and delayed separation, were investigated. While the effects of sheltering and delayed separation were found to slightly reduce the drag of very sparse canopies, the blockage effect significantly increased the drag of denser canopies ( λ≳0.04). An analogy between canopy flow and wall-confined flow around bluff bodies is used to identify an alternative reference velocity in the definition of the canopy drag coefficient; namely, the constricted cross-section velocity (Uc). Through comparison with both prior experimental data and the present numerical simulations, typical formulations for the drag coefficient of a single cylinder are shown to accurately predict the drag coefficient of staggered emergent canopies when Uc is used as the reference velocity. Finally, it is shown that this new model can be extended to predict the bulk drag coefficient of randomly arranged vegetation canopies.

The presence of large bottom roughness, such as that formed by benthic organisms on coral reef flats, has important implications for the size, concentration, and transport of suspended sediment in coastal environments. A 3 week field study was conducted in approximately 1.5 m water depth on the reef flat at Ningaloo Reef, Western Australia, to quantify the cross-reef hydrodynamics and suspended sediment dynamics over the large bottom roughness (∼20–40 cm) at the site. A logarithmic mean current profile consistently developed above the height of the roughness; however, the flow was substantially reduced below the height of the roughness (canopy region). Shear velocities inferred from the logarithmic profile and Reynolds stresses measured at the top of the roughness, which are traditionally used in predictive sediment transport formulations, were similar but much larger than that required to suspend the relatively coarse sediment present at the bed. Importantly, these stresses did not represent the stresses imparted on the sediment measured in suspension and are therefore not relevant to the description of suspended sediment transport in systems with large bottom roughness. Estimates of the bed shear stresses that accounted for the reduced near-bed flow in the presence of large roughness vastly improved the relationship between the predicted and observed grain sizes that were in suspension. Thus, the impact of roughness, not only on the overlying flow but also on bed stresses, must be accounted for to accurately estimate suspended sediment transport in regions with large bottom roughness, a common feature of many shallow coastal ecosystems.

Here we synthesize data from previous field and laboratory studies describing how rates of nutrient uptake and metabolite exchange (mass transfer) are related to form drag and bottom stresses (momentum transfer). Re-analysis of this data shows that rates of mass transfer are highly correlated (r2 ≥ 0.9) with the root of the bottom stress τbot0.4 under both waves and currents, and only slightly higher under waves (~10%). The amount of mass transfer that can occur per unit bottom stress (or form drag) is influenced by morphological features ranging anywhere from millimeters to meters in scale; however, surface-scale roughness (millimeters) appears to have little effect on actual nutrient uptake by living reef communities. Although field measurements of nutrient uptake by natural reef communities agree reasonably well with predictions based on existing mass-momentum transfer relationships, more work is needed to better constrain these relationships for more rugose and morphologically complex communities.

We investigate the influence of wind stresses, stratification, and coastal mesoscale eddies on upwelling intensity, vertical nutrient fluxes, and phytoplankton biomass on the continental shelf off Ningaloo Reef in northwestern Australia during an austral spring-summer period. A three-dimensional (3-D) hydrodynamic model, ROMS (Regional Ocean Modeling System), was coupled with a four-component nitrogen-based biogeochemical NPZD model (Nitrogen Phytoplankton Zooplankton Detritus) to resolve the shelf circulation as well as the coupled nutrient and phytoplankton dynamics within a broad shelf region surrounding Ningaloo Reef. The simulated currents, temperatures, and chlorophyll a concentrations generally agreed well with both the remotely sensed satellite images and observational data collected during a field experiment from September to November 2010. Scenario tests for an individual wind-driven upwelling event under a variety of hypothetical physical forcing conditions showed that shelf currents and biogeochemical variables were largely a function of wind stress and stratification. However, the functional relationships derived from this single wind event could not be extrapolated to other periods of the upwelling season, due to the additional influence of 3-D mesoscale processes on the shelf. The presence, intensification, and propagation of a coastal anticyclonic eddy during the study period strongly influenced the spatial and temporal variations in nutrient profiles, which in turn caused fluctuations in vertical nutrient fluxes that were largely independent of wind stress. These results emphasize that it is necessary to fully capture the 3-D details of the mesoscale and submesoscale coastal dynamics to properly predict upwelling-induced coastal phytoplankton dynamics in eddy-intensive shelf regions such as Ningaloo Reef.

The Regional Ocean Modeling System (ROMS) was applied to the Australian North-West Shelf (NWS) to hindcast the ocean response to four intense historical tropical cyclones (TCs). While the four cyclones had very different trajectories across the NWS, all passed within 150 km of a long-term vertical mooring located on the continental shelf in 125 m depth. The observed ocean response at this relatively shallow, Southern Hemisphere shelf site was characterized by the development of a peak in the counter-clockwise (CCW) near-inertial kinetic energy, mixed layer deepening, and subsequent restratification. Strong near-inertial isotherm oscillations were also observed following two of the cyclones. ROMS reproduced these features and also showed that the peak in the near-inertial CCW kinetic energy was observed on the left side of each cyclone trajectory. The time rate of change of near-inertial kinetic energy depended strongly on the storm Rossby number, i.e., defined based on the storm speed, the storm length scale, and the Coriolis frequency. The shallow water depth on the NWS resulted in first, a more rapid decay of near-inertial oscillations than in the deep ocean, and second a generation efficiency (the ratio of near-inertial power to the rate of wind work) of up to 10%, smaller than found for cyclones propagating across deeper water. The total energy put into near-inertial motions is nevertheless large compared to the background tidal energy. The rapid decay of near-inertial motions emphasizes the importance of frictional effects in characterizing the response to cyclone forcing in shallow seas.

A 2 week field experiment investigated the hydrodynamics of a strongly tidally forced tropical intertidal reef platform in the Kimberley region of northwestern Australia, where the spring tidal range exceeds 8 m. At this site, the flat and wide (∼1.4 km) reef platform is located slightly above mean sea level, such that during low tide the offshore water level can fall 4 m below the platform. While the reef always remained submerged over each tidal cycle, there were dramatic asymmetries in both the water levels and velocities on the reef, i.e., the flood duration lasted only ∼2 h versus ∼10 h for the ebb. These dynamics were investigated using a one-dimensional numerical model (SWASH) to solve the nonlinear shallow water equations with rapid (sub to supercritical) flow transitions. The numerical model revealed that as water drains off the reef, a critical flow point was established near the reef edge prior to the water discharging down the steep forereef. Despite this hydraulic control, bottom friction on the reef was still found to make a far greater contribution to elevating water levels on the reef platform and keeping it submerged over each tidal cycle. Finally, a simple analytical model more broadly shows how water levels on intertidal reef platforms functionally depend on properties of reef morphology, bottom roughness, and tidal conditions, revealing a set of parameters (a reef draining time-scale and friction parameter) that can be used to quantify how the water depth will fall on a reef during ebb tide.

Received 19 July 2012; revised 21 January 2013; accepted 25 January 2013; published 11 March 2013. [1] The shelf circulation off Ningaloo Reef near the North West Cape of Western Australia is driven by complex interactions between the southward flowing Leeuwin Current and wind-driven currents that episodically reverse the coastal flow toward the north. The presence of these northward (equatorward) wind-driven currents is thought to make this section of coast one of the few locations along Western Australia to experience periodic coastal upwelling. We used a combination of field observations and numerical modeling to investigate the summer circulation and upwelling dynamics along Ningaloo Reef. We analyzed current and temperature profiles from moorings at four sites across the shelf and used two Regional Ocean Modeling System (ROMS) sub-models: (1) a coarser model of northwestern Australia forced by a global ocean model and (2) a nested fine-scale model of the Ningaloo region. This nesting significantly improved model skill as it included the offshore mesoscale dynamics that strongly influenced the shelf circulation off Ningaloo. The field observations revealed several northward flow reversals, accompanied by cooling of the coastal waters adjacent to Ningaloo, which were associated with strong northward wind events. Analysis of the coastal heat budget revealed that cooling events were primarily driven by upwelling, whereas warming of coastal waters during relaxation events resulted mostly from along-shelf advection of warm water from the north. Due to the combined effects of its relatively steep (~1/50 slope) shelf and strong summer stratification, upwelled water was sourced from the interior of the water column, likely influencing the sources and fluxes of nutrients to Ningaloo Reef.

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.

[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.