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.

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.