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Nearshore rocky reefs with scales of order 10–100 m are common along the world's coastline and often shape wave‐driven hydrodynamics and shoreline morphology in their lee. The interaction of waves with these reefs generally results in either two or four‐cell mean circulation systems (2CC and 4CC, respectively), with diverging flows behind the reefs and at the shoreline in the 2CC case and flows that diverge in the lee and converge at the shoreline in the 4CC case. By applying a phase‐resolving wave‐flow model to conduct a detailed analysis of mean momentum balances for waves interacting with nearshore reefs, we develop an understanding of the drivers of 2CC and 4CC flow dynamics and how they vary for different reef geometries and wave and water level conditions. The 2CC or 4CC patterns were primarily driven by alongshore pressure gradients toward the exposed (nonreef fronted) or reef‐fronted beach. These alongshore pressure gradients were dependent on the cross‐shore setup dynamics governed by the balance between pressure (i.e., related to the setup) and radiation stress gradients, and mean bottom stresses exerted on the water column. If shoreline wave setup in the lee of the reef was less than the exposed beach, a 4CC pattern developed with convergent flow at the shoreline in the lee of the reef; otherwise, a 2CC emerged with divergent flow at the shoreline. Across the parameter space investigated, reef roughness, distance to the shoreline, and beach slope were the three parameters most likely to change the flow patterns between 2CC and 4CC. Plain Language Summary: Small‐scale nearshore rocky reefs are found worldwide along a variety of sandy and rocky coastlines. Wave breaking over small reefs drives mean alongshore circulation patterns in their lee that may cause shoreline accretion or erosion. In this study, we apply a wave‐flow model to investigate the physical drivers of the mean currents in the lee of small reefs. The alongshore circulation was primarily driven by the differences of the mean water levels between the lee and the adjacent nonreef fronted beaches. Mean water levels increased by wave breaking; however, the onshore‐directed mean flows over the reef created offshore‐directed bottom stresses that reduced the mean water levels in the reef lee. If the shoreline mean water levels in the lee were less than the adjacent beach, alongshore currents that converged from the adjacent beaches toward the reefs were developed. If the shoreline mean water levels in the lee of the reef exceeded the adjacent beach, alongshore currents that diverged from the reef toward the adjacent beach occurred. The improved understanding of the circulation drivers developed in this study enhances our ability to characterize and predict wave‐driven flows in small‐scale nearshore reef systems. Key Points: Phase‐resolved model simulations were used to understand circulation patterns that occur in the lee of small‐scale reefsTwo‐cell and four‐cell circulation patterns were primarily driven by alongshore pressure gradients, which depend on the setup dynamicsA four‐cell pattern generally developed if the shoreline wave setup in the lee of the reef was less than the adjacent nonreef fronted beach [ABSTRACT FROM AUTHOR]

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]

Two-dimensional mean wave-driven flow and setup dynamics were investigated at a reef-lagoon system at Ningaloo Reef, Western Australia, using the numerical wave-flow model, SWASH. Phase-resolved numerical simulations of the wave and flow fields, validated with highly detailed field observations (including >10 sensors through the energetic surf zone), were used to quantify the main mechanisms that govern the mean momentum balances and resulting mean current and setup patterns, with particular attention to the role of nonlinear wave shapes. Momentum balances from the phaseresolved model indicated that onshore flows near the reef crest were primarily driven by the wave force (dominated by radiation stress gradients) due to intense breaking, whereas the flow over the reef flat and inside the lagoon and channels was primarily driven by a pressure gradient. Wave setup inside the lagoon was primarily controlled by the wave force and bottom stress. The bottom stress reduced the setup on the reef flat and inside the lagoon. Excluding the bottom stress contribution in the setup balance resulted in an over prediction of the wave-setup inside the lagoon by up to 200--370%. The bottom stress was found to be caused by the combined presence of onshore directed wave-driven currents and (nonlinear) waves. Exclusion of the bottom stress contribution from nonlinear wave shapes led to an over prediction of the setup inside the lagoon by approximately 20--40%. The inclusion of the nonlinear wave shape contribution to the bottom stress term was found to be particularly relevant in reef regions that experience a net onshore mass flux over the reef crest. [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]

The article lists 2019 periodical reviewers including Katherine Adams, Sean Bailey, and Scott Bachman.

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. Plain Language Summary: Aquatic plants that grow in estuaries and coastal oceans (such as seagrass, kelp, and mangroves) have a considerable influence on water flow (currents) and on waves propagating toward the shore. However, mean flows generated by the waves interacting with aquatic vegetation (with time scales much longer than the individual wave periods) have not been comprehensively studied. This study provides a description of how submerged vegetation alters the mean wave‐driven flow structure. A combination of detailed experiments conducted in a wave flume and numerical simulations are used to show that the mean flow just above the vegetation is relatively strong (up to 20% to 50% of the maximum wave velocity above the canopy), while it is considerably weaker inside the vegetation. We identified three forces that govern the mean current profile: the wave Reynolds stress gradient, the turbulent Reynolds stress gradient, and the vegetation drag force. These forces are usually not accurately described in larger‐scale computer simulations of coastal processes. However, reliable simulation of processes in the coastal ocean such as sediment transport and nutrient exchange requires an accurate prediction of mean flows, and thus these forces need to be properly incorporated in computer models when applied to regions with aquatic vegetation. Key Points: Physical and numerical modeling is used to investigate the wave‐induced mean flow profiles in the presence of submerged vegetationThe multilayered phase‐resolving wave‐ flow model was able to accurately reproduce the depth variation of the wave‐driven mean flow profilesWave‐driven mean flows inside vegetation canopies are driven by vertical gradients in the wave and turbulent Reynolds stresses [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]

Similar to the construction of physical ships and laboratory buildings, scientific knowledge is built incrementally and requires solid components of data, theory, and methodology at each phase of the "construction." The peer‐review process provides the necessary "inspection" and the assurance that every step of the construction is solid, particularly in regard to the proper use of the scientific method. The peer‐review process helps improve the published work by providing constructive suggestions and by safeguarding against scientific work that could later be found to be built on shaky foundations. Because no single scientist has intimate knowledge of today's many aspects of the Ocean Sciences, we rely on each other's expertise to serve as unbiased "inspectors" of published articles. Your considerable time and effort, spent reviewing JGR‐Oceans manuscript(s) during 2017, are sincerely appreciated by our editorial board and by the Ocean Science community at large. We thank you for rising to this professional challenge and for your wisdom, commitment, skill, and service. Plain Language Summary: Similar to the construction of physical ships and laboratory buildings, scientific knowledge is built incrementally and requires solid components of data, theory, and methodology at each phase of the "construction". The peer review process provides the necessary "inspection" and the assurance that every step of the construction is solid, particularly in regard to the proper use of the scientific method. The peer‐review process helps improve the published work by providing constructive suggestions, and by safe‐guarding against scientific work that could later found to be built on shaky foundations. Because no single scientist has intimate knowledge of today's many aspects of the Ocean Sciences, we rely on each other's expertise to serve as unbiased "inspectors" of published articles. Your considerable time and effort, spent reviewing JGR‐Oceans manuscript(s) during 2017, are sincerely appreciated by our editorial board, and by the Ocean Science community at large. We thank you for rising to this professional challenge, and for your wisdom, commitment, skill, and service. Key Point: The JGR‐Oceans Editors thank all the peer reviewers from 2017 [ABSTRACT FROM AUTHOR]

Abstract: 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 hot spots), 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 data set, 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 interannual variability of the tropical cyclone‐induced sediment dynamics with greater suspended transport during the three consecutive Ningaloo Niño years (2011–2013) where sea surface temperatures off northwestern Australia were anomalously warm with elevated tropical cyclone activity. [ABSTRACT FROM AUTHOR]

Abstract: Two marine heat wave events along Western Australia (WA) during the alternate austral summer periods of 2010/2011 and 2012/2013, both linked to La Niña conditions, severely impacted marine ecosystems over more than 12° of latitude, which included the unprecedented bleaching of many coral reefs. Although these two heat waves were forced by similar large‐scale climate drivers, the warming patterns differed substantially between events. The central coast of WA (south of 22°S) experienced greater warming in 2010/2011, whereas the northwestern coast of WA experienced greater warming in 2012/2013. To investigate how oceanic and atmospheric heat exchange processes drove these different spatial patterns, an analysis of the ocean heat budget was conducted by integrating remote sensing observations, in situ mooring data, and a high‐resolution (∼1 km) ocean circulation model (Regional Ocean Modeling System). The results revealed substantial spatial differences in the relative contributions made by heat advection and air‐sea heat exchange between the two heat wave events. During 2010/2011, anomalous warming driven by heat advection was present throughout the region but was much stronger south of 22°S where the poleward‐flowing Leeuwin Current strengthens. During 2012/2013, air‐sea heat exchange had a much more positive (warming) influence on sea surface temperatures (especially in the northwest), and when combined with a more positive contribution of heat advection in the north, this can explain the regional differences in warming between these two La Niña‐associated marine heat wave events. [ABSTRACT FROM AUTHOR]

Abstract: Owing to their strong forcing at the air‐sea interface, tropical cyclones are a major driver of hydrodynamics and sediment dynamics of continental shelves, strongly impacting marine habitats and offshore industries. Despite the North West Shelf of Australia being one of the most frequently impacted tropical cyclone regions worldwide, there is limited knowledge of how tropical cyclones influence the sediment dynamics of this shelf region, including the significance of these episodic extreme events to the normal background conditions that occur. Using an extensive 2 year data set of the in situ sediment dynamics and 14 yearlong calibrated satellite ocean‐color data set, we demonstrate that alongshore propagating cyclones are responsible for simultaneously generating both strong wave‐induced sediment resuspension events and significant southwestward subtidal currents. Over the 2 year study period, two particular cyclones (Iggy and Narelle) dominated the sediment fluxes resulting in a residual southwestward sediment transport over the southern part of the shelf. By analyzing results from a long‐term (37 year) wind and wave hindcast, our results suggest that at least 16 tropical cyclones had a strong potential to contribute to that southwestward sediment pathway in a similar way to Iggy and Narelle. [ABSTRACT FROM AUTHOR]