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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 Acroporawithin 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.

Many low‐elevation, coral reef‐lined, tropical coasts are vulnerable to the effects of climate change, sea level rise, and wave‐induced flooding. The considerable morphological diversity of these coasts and the variability of the hydrodynamic forcing that they are exposed to make predicting wave‐induced flooding a challenge. A process‐based wave‐resolving hydrodynamic model (XBeach Non‐Hydrostatic, “XBNH”) was used to create a large synthetic database for use in a “Bayesian Estimator for Wave Attack in Reef Environments” (BEWARE), relating incident hydrodynamics and coral reef geomorphology to coastal flooding hazards on reef‐lined coasts. Building on previous work, BEWARE improves system understanding of reef hydrodynamics by examining the intrinsic reef and extrinsic forcing factors controlling runup and flooding on reef‐lined coasts. The Bayesian estimator has high predictive skill for the XBNH model outputs that are flooding indicators, and was validated for a number of available field cases. It was found that, in order to accurately predict flooding hazards, water depth over the reef flat, incident wave conditions, and reef flat width are the most essential factors, whereas other factors such as beach slope and bed friction due to the presence or absence of corals are less important. BEWARE is a potentially powerful tool for use in early warning systems or risk assessment studies, and can be used to make projections about how wave‐induced flooding on coral reef‐lined coasts may change due to climate change. Low‐lying tropical coasts fronted by coral reefs are threatened by the effects of climate change, sea level rise, and flooding caused by waves. However, the reefs on these coasts differ widely in their shape, size, and physical characteristics; the wave and water level conditions affecting these coastlines also vary in space and time. These factors make it difficult to predict flooding caused by waves along coral reef‐lined coasts. We created a system (“BEWARE”) that estimates how different wave, water level, and reef combinations can lead to flooding. This tool tells us what information is needed to make good predictions of flooding. We found that information on water levels and waves is most important, followed by the width of the reef. BEWARE can be used to make short‐term predictions of flooding in early warning systems, or long‐term predictions of how climate change will affect flooding caused by waves on coral reef‐lined coasts. Created large synthetic data set relating hydrodynamics, geomorphology, and runup on reef‐lined coastsOffshore forcing and reef width are the dominant controls of the hydrodynamic response on the reefPotential application in early warning systems and climate change impact assessments

A plethora of physical parameters, such as hydro-, litho- and morpho-dynamic characteristics, are essential for understanding the response of coastal systems to intense sea states in terms of sediment transport and shoreline evolution. Nowadays, numerical models are extensively applied to meet the above needs and support coastal planning and management. In the present work, a 2DH dynamic modelling system is used for simulating the hydrodynamic and meteorological/oceanographic characteristics of the Saronic Gulf, in order to examine circulation patterns and predict sediment transport phenomena under high wave conditions at the coast of Varkiza, a sandy beach in the southern Attica, Greece. Time series of wind and wave data were used as input at the open boundaries of the model domain while the model was calibrated and validated through (linear and directional) statistical measures with respect to in situwave measurements, since there was lack of hydrodynamic data at the site of interest. The simulation period of the model was between January 3 and February 19, 2013, with consecutive high waves in-between. The good agreement of the numerical results from the wave and hydrodynamic model with in situmeasurements confirmed the suitability of the model for the support of sediment transport rates at Varkiza coastal segment. Model results reveal that there is a counter-clockwise water circulation during high waves that contribute to the erosion of the examined beach, which is also confirmed by independent field measurements.