A Numerical Study of Wave‐Driven Mean Flows and Setup Dynamics at a Coral Reef‐Lagoon System

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 phase‐resolved 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. Coral reefs that are located in close proximity to a coastline are typically characterized by a steep slope and reef crest that is connected to the coast or front a shallow lagoon. At the reef crest, waves break and drive onshore‐directed currents and elevate the mean (time‐averaged) water level in the lagoon. In this study, we combined measurements of waves, currents and water levels with simulations from an advanced computer model to understand the physical mechanisms that determine the current patterns and water level variations at a coral reef‐lagoon system in Western Australia. Friction generated by the water moving over the rough reef structures was found to reduce the mean water levels inside the lagoon. This friction was explained by the combined presence of both waves and mean currents. Furthermore, near the reef crest, the waves peak and pitch forward before they break, and this nonlinear wave shape was found to enhance the friction from the bottom. This contribution from nonlinear wave shapes however, is generally not accurately described in larger‐scale computer models and should be included in such computer models to provide more reliable simulations of the water motion in coral reefs. The numerical wave‐flow model, SWASH, reproduced highly detailed field measurements of waves and currents through the surf zone of a reef‐lagoon system (Ningaloo Reef, AU)Wave setup inside the lagoon was reduced by bottom stresses generated by the combined action of waves and currentsExclusion of the bottom stress contribution from nonlinear wave shapes resulted in a 20%–40% over prediction of the setup inside the lagoon The numerical wave‐flow model, SWASH, reproduced highly detailed field measurements of waves and currents through the surf zone of a reef‐lagoon system (Ningaloo Reef, AU) Wave setup inside the lagoon was reduced by bottom stresses generated by the combined action of waves and currents Exclusion of the bottom stress contribution from nonlinear wave shapes resulted in a 20%–40% over prediction of the setup inside the lagoon