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Wave breaking on the steep fore‐reef slopes of shallow fringing reefs can be effective at dissipating incident sea‐swell waves prior to reaching reef shorelines. However, wave setup and free infragravity waves generated during the sea‐swell breaking process are often the largest contributors to wave‐driven water levels (wave runup) at the shoreline. Laboratory flume experiments and a two‐dimensional vertical phase‐resolving nonhydrostatic wave‐flow model, which includes a canopy model to predict drag forces generated by roughness elements, were used to investigate wave‐driven water levels for along‐shore uniform fringing reefs. In contrast to many previous studies, both the laboratory experiment and the numerical model account for the effects of large bottom roughness. The numerical model reproduced the observations of the wave transformation and runup over both smooth and rough reef profiles. The numerical model was then extended to quantify the influence of reef geometry and compared to simulations of plane beaches lacking a reef. For a fixed offshore forcing condition, the fore‐reef slope controlled wave runup on reef‐fronted beaches, whereas the beach slope controlled wave runup on plane beaches. As a result, the coastal protection utility of reefs is dependent on these slopes. For our examples, with a fore‐reef slope of 1/5 and a 500 m prototype reef flat length, a beach slope of ∼1/30 marked the transition between the reef providing runup reduction for steeper beach slopes and enhancing wave runup for milder slopes. Roughness coverage, spacing, dimensions, and drag coefficient were investigated, with results indicating the greatest runup reductions were due to tall roughness elements on the reef flat. Plain Language Summary: Wave breaking and bottom friction are effective at reducing incident sea‐swell waves before they can reach the shoreline of reef‐fronted coastlines. However, globally, mass mortality of coral reef‐building organisms is causing coral reefs to become structurally flatter, a process that may lower wave dissipation. Laboratory flume experiments and a multilayer phase‐resolving wave‐flow model that includes drag forces generated by roughness elements (representing coral reef forms) were used to investigate wave‐driven water levels in the lee of fringing reefs and assess the influence of reef geometry and roughness characteristics. The numerical model was able to reproduce laboratory observations of waves and water levels over both smooth and rough reef profiles. Wave runup, the vertical extent of wave uprush on a beach, was sensitive to the presence and characteristics of roughness. Roughness coverage, spacing, and dimensions were investigated with results indicating the greatest runup reductions were due to tall roughness elements on the reef flat. Key Points: SWASH reproduced laboratory observations of waves and runup over both smooth and rough fringing reefsFore‐reef slope controls wave runup on reef‐fringed coasts as opposed to beach slope on plane open coast beachesWave runup was sensitive to bottom roughness with tall roughness elements on the reef flat generating the greatest runup reduction [ABSTRACT FROM AUTHOR]

An accurate representation of physical and biological processes is crucial to resolve larval dispersal pathways and characterize connectivity of coral reef ecosystems. We investigate how hydrodynamic forcings drive larval retention rates during the bi‐annual mass coral spawning of the coral genus Acropora within a coral reef atoll (Mermaid Reef), located off northwestern Australia. By analyzing hydrodynamic conditions during 41 yr of historical spring and autumn coral spawning events, we identify typical and extreme hydrodynamic forcing conditions. Particle tracking using the output from a fine‐scale coupled wave‐flow hydrodynamic model forced with typical hydrodynamic conditions during coral spawning, revealed a mean transport of larvae eastward across the atoll. Transport was mainly driven by a combination of wave and tidal currents, where the residual tidal flow and unidirectional wave flow increased the net export of particles, and the oscillatory tidal (non‐residual) flow reduced the net export of particles from the reef. Importantly, however, numerical simulations forced with extreme hydrodynamic conditions generated by episodic tropical cyclones (11 out of 41 yr) showed large deviations from the typical eastward flow during autumn spawning, generating different connectivity pathways within the reef. Considering the substantial time larvae can be retained within reef systems, overlooking fine‐scale hydrodynamic processes may greatly overestimate larval transport distances between adjacent coral reef atolls. As a result, we emphasize the need to consider fine‐scale hydrodynamic processes within regional connectivity predictions, which is generally not considered yet critical to understand the capacity of reefs to recover following disturbances. [ABSTRACT FROM AUTHOR]

Coral reefs generate substantial volumes of carbonate sediment, which is redistributed throughout the reef‐lagoon system. However, there is little understanding of the specific processes that transport this sediment produced on the outer portions of coral reefs throughout a reef‐lagoon system. Furthermore, the separate contributions of currents, sea‐swell waves, and infragravity waves to transport, which are all strongly influenced by the presence of a reef, is not fully understood. Here, we show that in reef‐lagoon systems most suspended sediment is transported close to the seabed and can, at times, be suspended higher in the water column during oscillatory flow transitions (i.e., near slack flow) at sea‐swell wave frequencies, and during the peak onshore oscillatory velocity phase at infragravity wave frequencies. While these wave frequencies contribute to the transport of suspended sediment offshore and onshore, respectively, the net flux is small. Mean currents are the primary transport mechanism and responsible for almost 2 orders of magnitude more suspended‐sediment flux than sea‐swell and infragravity waves. Whilst waves may not be the primary mechanism for the transport of sediment, our results suggest they are an important driver of sediment suspension from the seabed, as well as contributing to the partitioning of sediment grain sizes from the reef to the shoreline. As the ocean wave climate changes, sea level rises, and the composition of reef benthic communities change, the relative importance of mean currents, sea‐swell waves, and infragravity waves is likely to change, and this will affect how sediment is redistributed throughout reef‐lagoon systems. Plain Language Summary: Most of the sandy sediment found on coral reef coastlines is produced by organisms living within the reef. This sediment is then transported by waves and currents across the reef and distributed throughout the lagoon. Little is known about these transport processes, including the relative importance of how currents or different types of waves drive transport. This study shows that most of the sediment in the water column (suspended sediment) is transported close to the seabed by mean currents. At times, this sediment can be suspended higher in the water column by short waves (5–25 s) when the flow transitions from being onshore directed to offshore directed, or when the velocities of longer period waves (25–250 s), called infragravity waves, are directed onshore. The timing of the suspension by these waves helps to sort the sediment into different sizes across the system, but the quantity of sediment transported is small. As the ocean wave climate changes, sea level rises, and reefs change, the relative importance of mean currents, sea‐swell waves, and infragravity waves is also likely to change, and this will affect how sediment is redistributed throughout reef‐lagoon systems. This study provides insight into what changes may be expected. Key Points: Sediment transported in suspension is 3–4 times lower than sediment transported as bedloadSediment transported in suspension by mean currents is 2 orders of magnitude greater than sediment transported by wavesSea‐swell waves typically transport sediment offshore and infragravity waves and mean currents typically transport sediment onshore [ABSTRACT FROM AUTHOR]

Interactions between oceanic and atmospheric processes within coral reefs can significantly alter local-scale (< km) water temperatures, and consequently drive variations in heat stress and bleaching severity. The Scott Reef atoll system was one of many reefs affected by the 2015–2016 mass coral bleaching event across tropical Australia, and specifically experienced sea surface temperature anomalies of 2 °C that caused severe mass bleaching (> 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. [ABSTRACT FROM AUTHOR]

Benthic fluxes of dissolved nutrients in reef communities are controlled by oceanographic forcing, including local hydrodynamics and seasonal changes in oceanic nutrient supply. Up to a third of reefs worldwide can be characterized as having circulation that is predominantly tidally forced, yet almost all previous research on reef nutrient fluxes has focused on systems with wave-driven circulation. Fluxes of dissolved nitrogen and phosphorus were measured on a strongly tide-dominated reef platform with a spring tidal range exceeding 8 m. Nutrient fluxes were estimated using a one-dimensional control volume approach, combining flow measurements with modified Eulerian sampling of waters traversing the reef. Measured fluxes were compared to theoretical mass-transfer-limited uptake rates derived from flow speeds. Reef communities released 2.3 mmol m -2 d -1 of nitrate, potentially derived from the remineralization of phytoplankton and dissolved organic nitrogen. Nutrient concentrations and flow speeds varied between the major benthic communities (coral reef and seagrass), resulting in spatial variability in estimated nitrate uptake rates. Rapid changes in flow speed and water depth are key characteristics of tide-dominated reefs, which caused mass-transfer-limited nutrient uptake rates to vary by an order of magnitude on timescales of ∼ minutes–hours. Seasonal nutrient supply was also a strong control on reef mass-transfer-limited uptake rates, and increases in offshore dissolved inorganic nitrogen concentrations during the wet season caused an estimated twofold increase in uptake. [ABSTRACT FROM AUTHOR]

Scott Reef is a remote yet biodiverse coral reef atoll, rising from depths > 1000 m on the edge of the continental shelf of northwestern Australia. An intensive 2‐week field study was conducted to assess how physical oceanographic processes influence reef communities in South Scott's deep (~ 50 m) and expansive (~ 300 km2) semi‐enclosed lagoon. The study covered a spring–neap tidal cycle, during which moored instruments measured temperature and velocities at a lagoon entrance and ship‐based vertical profilers measured water quality parameters. Tidally driven internal bores advected cooler and deeper offshore waters (up to 4.5°C, mean 2.4°C) into the lagoon, which were also richer in nutrients and chlorophyll a than lagoon waters. This offshore water originated from approximately 75 m depth. We used the strong observed relationship between in situ measurements of nitrate and temperature to estimate nitrate concentrations from high temporally and spatially resolved temperature measurements at the lagoon entrance, and then estimated the horizontal nitrate fluxes into the lagoon using the velocity measurements. The depth‐integrated, time‐averaged nitrate flux during spring tides (1.46 kg m−1 d−1) was over three times larger than during neap tides (0.46 kg m−1 d−1), despite a passing tropical storm that temporarily deepened the offshore thermocline and reduced the magnitude of the fluxes. Our observations indicate that colder, deeper, and nutrient‐rich water associated with internal tidal bores during spring tide is likely to be the primary mechanism through which allochtonous nutrients are delivered to benthic and pelagic communities within the lagoon of this isolated atoll. [ABSTRACT FROM AUTHOR]

The hydrodynamics of a tidally forced semi‐enclosed coral reef atoll (North Scott) at the edge of the continental shelf of northwestern Australia were investigated by combining field observations and numerical modeling. The observations revealed that the spring tidal range outside the atoll reaches 4 m, and as the water level drops below mean sea level, the reef rim surrounding the shallow (~10–15 m) lagoon becomes exposed. During this time, the lagoon can only exchange with the open ocean through two narrow channels, resulting in highly asymmetric water levels and velocities that were most pronounced during spring tide. On average, the ebb tide duration was ~2 hr longer than the flood, with rapid flood velocities in the channel reaching 2 m/s. We applied an unstructured grid model Delft3D‐Flexible Mesh to simulate the atoll hydrodynamics and were able to replicate the asymmetric water levels and complex velocities in the lagoon. The results revealed that at higher tidal stages, a dominant momentum balance exists between the pressure gradient (established by the propagation of the tide on the shelf) and the local flow acceleration of water throughout the interior of the atoll. At lower tidal stages, which coincided with a reversal of the offshore tidal pressure gradient, the lagoon became isolated from offshore dynamics and all momentum terms were negligible. This resulted in a tidally averaged residual westward flow within the lagoon that drove an asymmetric flushing pattern within the atoll, which we propose would be a common flushing mechanism within other tide‐dominated atolls worldwide. Key Points: The hydrodynamics of a tide‐dominated atoll reef system were assessed with field observations and numerical modelingThe semi‐enclosed atoll morphology and large tidal range resulted in highly asymmetric water levels, velocities, and residual flowsA residual east‐west flow, caused by interactions between the phasing of the ocean tide and lagoon water levels, dominated flushing [ABSTRACT FROM AUTHOR]

Benthic fluxes of dissolved nutrients in reef communities are controlled by oceanographic forcing including hydrodynamic regime and seasonal changes in oceanic nutrient supply. Up to a third of reefs worldwide can be characterised as having circulation that is tidally-driven, yet almost all previous research on reef nutrient fluxes has focused on systems with wave-driven circulation. Fluxes of dissolved nitrogen and phosphorus were measured on a strongly tide-dominated (spring range > 8 m) reef platform located in the Kimberley region of northwest Australia. A one-dimensional control volume approach was used, which combines continuous measurements of flow with modified Eulerian sampling of waters traversing the reef. Measured fluxes were compared to theoretical mass-transfer-limited uptake rates derived from flow speeds. Reef communities released a moderate amount of nitrate, potentially derived from the remineralization of phytoplankton and dissolved organic nitrogen. Nutrient concentrations and flow speeds varied between the major benthic communities (coral reef and seagrass), resulting in spatial variability in estimated nitrate uptake rates. Rapid changes in flow speed and water depth are key characteristics of tide-dominated reefs, which caused mass-transfer-limited nutrient uptake rates to vary by an order of magnitude on time scales of ~minutes-hours. Seasonal nutrient supply was also a strong control on reef mass-transfer-limited uptake rates, and increases in offshore dissolved inorganic nitrogen concentrations during the wet season caused an estimated twofold increase in uptake. [ABSTRACT FROM AUTHOR]

The effect of bottom roughness on setup dynamics was investigated using high-resolution observations across a laboratory fringing reef profile with roughness elements scaled to mimic the frictional wave dissipation of a coral reef. Results with roughness were compared with smooth bottom runs across 16 offshore wave and still water level conditions. The time-averaged and depth-integrated force balance was evaluated from observations collected at 17 locations along the flume and consisted of cross-shore pressure and radiation stress gradients whose sum was balanced by quadratic mean bottom stresses. The introduction of roughness had two primary effects. First, for runs with roughness, frictional wave dissipation occurred on the reef slope offshore of the breakpoint, reducing wave heights prior to wave breaking. Second, offshore-directed mean bottom stresses were generated by the interaction of the combined wave-current velocity field with the roughness elements. These two mechanisms acted counter to one another. Frictional wave dissipation resulted in radiation stress gradients that were predicted to generate 18% (on average) less setup on the reef flat for rough runs than for smooth runs when neglecting mean bottom stresses. However, mean bottom stresses increased the predicted setup by 16% on average for runs with roughness. As a result, setup on the reef flat was comparable (7% mean difference) between corresponding rough and smooth runs. These findings are used to assess prior results from numerical modeling studies of reefs and also to discuss the broader implications for how large roughness influences setup dynamics in the nearshore zone. [ABSTRACT FROM AUTHOR]

A Lagrangian particle tracking model driven by a regional ocean circulation model was used to investigate the seasonally varying connectivity patterns within the shelf circulation surrounding the 300 km long Ningaloo Reef in Western Australia (WA) during 2009–2010. Forward-in-time simulations revealed that surface water was transported equatorward and offshore in summer due to the upwelling-favorable winds. In winter, however, water was transported polewards down the WA coast due to the seasonally strong Leeuwin Current. Using backward-in-time simulations, the subsurface transport pathways revealed two main source regions of shelf water reaching Ningaloo Reef: (1) a year-round source to the northeast in the upper 100 m of water column; and (2) during the summer, an additional source offshore and to the west of Ningaloo in depths between ~30 and ~150 m. Transient wind-driven coastal upwelling, onshore geostrophic transport and stirring by offshore eddies were identified as the important mechanisms influencing the source water origins. The identification of these highly time-dependent transport pathways and source water locations is an essential step towards quantifying how key material (e.g., nutrients, larvae, contaminants, etc.) is exchanged between Ningaloo Reef and the surrounding shelf ocean, and how this is mechanistically coupled to the complex ocean dynamics in this region. [ABSTRACT FROM AUTHOR]

High-resolution observations from a 55-m-long wave flume were used to investigate the dynamics of wave setup over a steeply sloping reef profile with a bathymetry representative of many fringing coral reefs. The 16 runs incorporating a wide range of offshore wave conditions and still water levels were conducted using a 1:36 scaled fringing reef, with a 1:5 slope reef leading to a wide and shallow reef flat. Wave setdown and setup observations measured at 17 locations across the fringing reef were compared with a theoretical balance between the local cross-shore pressure and wave radiation stress gradients. This study found that when radiation stress gradients were calculated from observations of the radiation stress derived from linear wave theory, both wave setdown and setup were underpredicted for the majority of wave and water level conditions tested. These underpredictions were most pronounced for cases with larger wave heights and lower still water levels (i.e., cases with the greatest setdown and setup). Inaccuracies in the predicted setdown and setup were improved by including a wave-roller model, which provides a correction to the kinetic energy predicted by linear wave theory for breaking waves and produces a spatial delay in the wave forcing that was consistent with the observations. [ABSTRACT FROM AUTHOR]

A laboratory experiment was conducted to investigate the dynamics of cross-shore sediment transport across a fringing coral reef. The aim was to quantify how a highly bimodal spectrum of high-frequency (sea-swell) and low-frequency (infragravity and seiching) waves that is typically present on coral reef flats, influences the various sediment transport mechanisms. The experiments were conducted in a 55 m wave flume, using a 1:15 scale fringing reef model that had a 1:5 forereef slope, a 14 m long reef flat, and a 1:12 sloping beach. The initial 7 m of reef flat had a fixed bed, whereas the back 7 m of the reef and the beach had a moveable sandy bed. Four seven-hour irregular wave cases were conducted both with and without bottom roughness elements (schematically representing bottom friction by coral roughness), as well as for both low and high still water levels. We observed that the wave energy on the reef flat was partitioned between two primary frequency bands (high and low), and the proportion of energy within each band varied substantially across the reef flat, with the low-frequency waves becoming increasingly important near the shore. The offshore transport of suspended sediment by the Eulerian mean flow was the dominant transport mechanism near the reef crest, but a wide region of onshore transport prevailed on the reef flat where low-frequency waves were very important to the overall transport. Ripples developed over the movable bed and their properties were consistent with the local high-frequency wave orbital excursion lengths despite substantial low-frequency wave motions also present on the reef flat. This study demonstrated that while a proportion of the sediment was transported by bedload and mean flow, the greatest contributions to cross-shore transport were due to the skewness and asymmetry of the high and low-frequency waves. [ABSTRACT FROM AUTHOR]

We present a three-dimensional hydrodynamic-biogeochemical model of a wave-driven coral-reef lagoon system using the circulation model ROMS (Regional Ocean Modeling System) coupled with the wave transformation model SWAN (Simulating WAves Nearshore). Simulations were used to explore the sensitivity of water column carbonate chemistry across the reef system to variations in benthic reef metabolism, wave forcing, sea level, and system geomorphology. Our results show that changes in reef-water carbonate chemistry depend primarily on the ratio of benthic metabolism to the square root of the onshore wave energy flux as well as on the length and depth of the reef flat; however, they are only weakly dependent on channel geometry and the total frictional resistance of the reef system. Diurnal variations in pCO2, pH, and aragonite saturation state (Ωar) are primarily dependent on changes in net production and are relatively insensitive to changes in net calcification; however, net changes in pCO2, pH, and Ωar are more strongly influenced by net calcification when averaged over 24 hours. We also demonstrate that a relatively simple one-dimensional analytical model can provide a good description of the functional dependence of reef-water carbonate chemistry on benthic metabolism, wave forcing, sea level, reef flat morphology, and total system frictional resistance. Importantly, our results indicate that any long-term (weeks to months) net offsets in reef-water pCO2 relative to offshore values should be modest for reef systems with narrow and/or deep lagoons. Thus, the long-term evolution of water column pCO2 in many reef environments remains intimately connected to the regional-scale oceanography of offshore waters and hence directly influenced by rapid anthropogenically driven increases in pCO2. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The article presents a study which examined the importance of particulate organic nitrogen (PON) and carbon (POC) in reef nutrient budgets over a fringing coral reef as important factors to determine phtoplankton production and mechanisms of supply at Ningaloo Reef in Western Australia. It is stated that sampling in different reef zones minimised flux estimates since the residence time over the reef is insufficient for pelagic phytoplankton production to significantly alter their concentrations. The mean currents within the circulation cell including hourly depth-averaged current speeds are explained.

The response of the circulation of a coral reef system in Kaneohe Bay, Hawaii, to incident wave forcing was investigated using field data collected during a 10-month experiment. Results from the study revealed that wave forcing was the dominant mechanism driving the circulation over much of Kaneohe Bay. As predicted theoretically, wave setup generated near the reef crest resulting from wave breaking established a pressure gradient that drove flow over the reef and out of the two reef channels. Maximum reef setup was found to be roughly proportional to the offshore wave energy flux above a threshold root-mean-square wave height of 0.7 m (at which height setup was negligible). On the reef flat, the wave-driven currents increased approximately linearly with incident wave height; however, the magnitude of these currents was relatively weak (typically <20 cm s-1) because of (i) the mild fore-reef slope of Kaneohe Bay that reduced setup resulting from a combination of frictional wave damping and its relatively wide surf zone compared to steep-faced reefs, and (ii) the presence of significant wave setup inside its coastally bounded lagoon, resulting from frictional resistance on the lagoon–channel return flows, which reduced cross-reef setup gradients by 60%–80%. In general, the dynamics of these wave-driven currents roughly matched predictions derived from quasi-one-dimensional mass and momentum balances that incorporated radiation stresses, setup gradients, bottom friction, and the morphological properties of the reef–lagoon system. [ABSTRACT FROM AUTHOR]

Coral reef islands are among the most vulnerable landforms to climate change. However, our understanding of their morphodynamics at intermediate (seasonal to interannual) timescales remains poor, limiting our ability to forecast how they will evolve in the future. Here, we applied a semi-automated shoreline detection technique (CoastSat.islands) to 20 years of publicly available satellite imagery to investigate the evolution of a group of reef islands located in the eastern Indian Ocean. At interannual timescales, island changes were characterized by the cyclical re-organization of island shorelines in response to the variability in water levels and wave conditions. Interannual variability in forcing parameters was driven by El Niño Southern Oscillation (ENSO) cycles, causing prolonged changes to water levels and wave conditions that established new equilibrium island morphologies. Our results present a new opportunity to measure intermediate temporal scale changes in island morphology that can complement existing short-term (weekly to seasonal) and long-term (decadal) understanding of reef island evolution. [ABSTRACT FROM AUTHOR]

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 s-1. 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 result in uncertainties in mass transfer coefficients of at most ±10% for the lobate coral form and ±5% for the branched coral forms. Measuring external turbulence in bulk flows is not necessary for most evaluations of biogeochemical rates in benthic reef systems. [ABSTRACT FROM AUTHOR]

The worlds' coral reefs are declining due to the combined effects of natural disturbances and anthropogenic pressures including thermal coral bleaching associated with global climate change. Nearshore corals are receiving increased anthropogenic stress from coastal development and nutrient run-off. Considering forecast increases in global temperatures, greater understanding of drivers of recovery on nearshore coral reefs following widespread bleaching events is required to inform management of local stressors. The west Pilbara coral reefs, with cross-shelf turbidity gradients coupled with a large nearby dredging program and recent history of repeated coral bleaching due to heat stress, represent an opportune location to study recovery from multiple disturbances. Mean coral cover at west Pilbara reefs was monitored from 2009 to 2018 and declined from 45% in 2009 to 5% in 2014 following three heat waves. Recruitment and juvenile abundance of corals were monitored from 2014 to 2018 and were combined with biological and physical data to identify which variables enhanced or hindered early-stage coral recovery of all hard corals and separately for the acroporids, the genera principally responsible for recovery in the short-term (<7 years). From 2014 to 2018, coral cover increased from 5 to 10% but recovery varied widely among sites (0–13%). Hard coral cover typically recovered most at shallower sites that had higher abundance of herbivorous fish, less macroalgae, and lower turbidity. Similarly, acroporid corals recovered most at sites with lower turbidity and macroalgal cover. Juvenile acroporid densities were a good indicator of recovery at least two years after they were recorded. However, recruitment to settlement tiles was not a good predictor of total coral or acroporid recovery. This study shows that coral recovery can be slower in areas of high turbidity and the rate may be reduced by local pressures, such as dredging. Management should focus on improving or maintaining local water quality to increase the likelihood of coral recovery under climate stress. Further, in turbid environments, juvenile coral density predicts early coral recovery better than recruits on tiles and may be a more cost-effective technique for monitoring recovery potential. • Three thermal anomalies over four years bleached corals and reduced cover by ~90%. • Coral recovery varied spatially, limited driven mostly by turbidity. • Better water quality increases the likelihood of coral recovery under climate stress. • Juvenile coral density predicted early coral recovery better than recruits on tiles. [ABSTRACT FROM AUTHOR]