Many tropical coastlines are fronted by coral reefs and are increasingly exposed to wave attack and wave-driven marine flooding. This problem demands immediate attention as safe habitability of and social and economic activity in reef-lined coastal regions are under serious threat, while these regions are known to have some of the world’s highest population densities.
High runup events and flooding on coral reef-lined coasts have been subject of recent studies, and some valuable insights are gained. It was found that the recent increases in wave attack, high runup events, and coastal flooding are primarily due to high offshore water levels coinciding with high energy swell events, circumstances which will become more frequent with sea-level rise. Increasing water depth over the reef changes the hydrodynamics across the reef in such a way that larger incident-band and infra gravity-band waves reach the shoreline, causing high runup levels and flooding of the land behind the shoreline.
However, little is known about the influence of longshore variations on runup and flooding of reef-lined coasts, while most show significant longshore variations, of which shore-normal paleo-stream channels are a prevalent one. This study aims to fill in that knowledge gap by examining the influence of paleo-stream channels on runup along reef-fronted shorelines, specifically during extreme wave conditions.
With a system analysis we determine the range of naturally occurring topographies of reef-channel systems and determine a representative reef. Results of this analysis are a useful starting point for future studies on this subject.
With a parametric study using the numeric model XBeach, we show that the presence of a channel results in a strong circulation on the reef flat and significant longshore variation of runup. Depending on the geometry and forcing, runup levels are increased next to the channel or inside the channel. This impact of the channel increases for higher incident waves, lower incident wave steepness, wider channels, a narrower reef and shorter channel spacing. Longshore variation of infragravity wave height is responsible for large scale variations in runup, while setup, short waves and very low frequency wave heights cause a local increase of runup inside the channel.
Results of the parametric study are valuable as they provide insight in which locations on a coast are most vulnerable to high runup events, using only widely available data such as reef geometry and offshore wave conditions. This is relevant for prediction of coastal hazards and to guide coastal management policies. Furthermore, this study provides insights for future studies on flood risk of reef-lined coasts, as it illustrates the importance of accounting for longshore variations while schematizing a coastline to predict high runup and coastal flooding, for instance to assess when a 1D schematization is sufficient and when a 2D model is required.

Coral reefs are degrading at an alarming rate, affecting not only the precarious coral ecosystem but also human habitat. The combination of coral degradation, sea level rise and its exacerbated effect in the tropics, and the possible storm intensification increases the flood vulnerability of low-lying tropical islands. To protect reef fronted coasts against flooding, coral restoration is put forward as measure to increase coastal safety. This study addresses the effects and efficiency of coral restoration in four steps. First, a simple reef hydrodynamic model is formulated to identify important drivers of runup at a reef fronted beach, to be used as a quick scan tool before using more intensive process-based models. Next, 30.000 US reef profiles are classified to gain insight into the prevalence of different reef shapes. Four dominant reef profiles are then used in the subsequent modeling step, in which the hydrodynamics and flood vulnerability of different reef shapes are investigated using the XBeach process-based model. With the knowledge gained, the hydrodynamic effects and runup reduction potential of different restoration configurations at various reef morphologies can be assessed.

Many tropical, coral reef-lined coasts, are low-lying with elevations less than five meters above mean sea level. Climate-change-driven sea level rise, coral reef decay and changes in (storm) wave climate will lead to greater chance and impacts of wave-driven flooding, posing a heavy threat to these coastal communities. Early warning systems (EWS) are effective for risk management and disaster reduction, however, the vast majority of the world's inhabitants of coral reef-lined coasts have no such system in place. Unfortunately, the complex hydrodynamics and bathymetry of reef-lined coasts make it difficult to establish a global flood prediction model for these areas. This thesis aims to develop a set of 'cluster profiles' that can be used to accurately represent coral reef-lined coasts around the globe. By representing an expansive variety of reef morphology, the cluster profiles are capable of predicting the wave runup over thousands of different coral reef profiles with a fraction of the number. The cluster profiles could be input into a tool such as a Bayesian probabilistic network which can be trained to provide real-time wave runup and flooding predictions given local bathymetry and offshore wave conditions, thus establishing a simplified global flooding EWS. The methodology includes two stages of data reduction. First, cluster analysis techniques are used to group thousands of coral reef profiles into 500 clusters based on morphology alone. Second, agglomerative hierarchical clustering is used to further group the profiles with similar morphology and wave runup response, resulting in a final set of 311 to 45 cluster profiles. Here we show that the cluster profiles are capable of predicting the wave runup for a set of 1000 reef profiles with a mean relative difference of approximately 10\%. The comparison was done using the numerical wave model XBeach with four different wave conditions. The methodology has been developed such that it could be expanded to other coastal environments. A summary of the methodology used in the study is illustrated on the following page.

Spurs-and-grooves (SAG) are a common and impressive characteristic of shallow fore reef areas worldwide. Although the existence and geometrical properties of SAG are well-documented ever since the 50’s, the literature concerning specifically the hydrodynamics around them is sparse. This study provides a characterization of the 3D flow patterns found on SAG formations, and a sensitivity of that flow for a set of short wave and SAG geometry parameters, as well as for alongshore and long wave forcing. Its main interest is to provide scientists predictive capability of the flow conditions for a set of conditions commonly found on coral reef systems with SAG formations. Delft3D-FLOW coupled with SWAN/XBeach (3D phase-averaged) was applied to model schematic SAG formations.

Shore-normal shoaling waves on top of SAG formations are shown to drive two circulations cells, the first in deeper waters with offshore spur and onshore groove depth-averaged velocities (offshore cell), and the second in shallower depths with offshore groove and onshore spur depth-averaged currents (onshore cell). In the offshore cell, the cross-shore velocity profile shows vertically monotonic currents - onshore to grooves and offshore to spurs -, except for the bottom, at which velocities are always onshore. In the onshore cell, the velocity profile shows offshore surface velocities and onshore bottom currents for both spur and groove, with resulting depth-averaged offshore groove and onshore spur velocities.

The mechanism driving this flow results from the wave forcing being mostly balanced by pressure gradients both in the cross-shore and alongshore, and the mismatch between those is balanced by horizontal turbulent forces, that are higher in deeper waters, and friction, larger in shallower waters. Variations of this pattern are associated with changes in the velocity profile, that fundamentally depend on the wave, SAG geometry and alongshore forcing parameters.

The waves are the main driving of the SAG flow, and as such wave parameters play a fundamental role in the SAG hydrodynamics.

Wave heights are the most important parameter associated with the flow strength - higher waves induce significantly stronger circulation cells. When wave heights start breaking due to depth limitation, the SAG circulation cell is lost, and the velocity profile shape starts having onshore surface and undertow with maximum values at mid depth.

Wave periods have moderate influence on the velocity values found on SAG circulation cells - higher wave periods induce slightly higher velocities. When the wave steepness reaches the breaking limit, the whitecapping results in changes of the velocity profile similarly to the case of depth-induced breaking waves.

The role of varying wave directions and directional spreadings could not be accurately evaluated due to uncertainties related to the importance of refraction and diffraction using a phase-averaged model. An initial assessment of their importance with a model neglecting refraction, thus with unchangeable wave direction, was performed. Results showed that oblique waves result in alongshore transport systems, i.e., cross-shore currents become significantly lower than in the alongshore. In those cases, the SAG offshore cell is lost, and the onshore cell gets wider and stronger.

The SAG geometry has a very important role associated with the resulting SAG hydrodynamics. Overall, the spur height, SAG wavelength and the SAG shape provide the biggest influence on the hydrodynamics.

The spur heights have significantly influence in the strength of SAG circulation cells - higher spur heights are associated with stronger flows.

The SAG wavelengths moderately influence the strength of the flow, with longer SAG wavelengths resulting in not much stronger SAG circulation cells. Shorter SAG wavelengths do not present the offshore SAG circulation cell, due to higher alongshore mixing of momentum that gives offshore spur and groove currents in that zone.

The shape of the SAG formations is, together with the wave heights, the most important parameter influencing the strength of the flow. SAG formations with peak spur height located further onshore (Buttress type) have SAG circulation with higher velocities involved and the zonation of the SAG circulation cells changes accordingly, i.e., lower peak spur height depths have circulation cells shifted onshore, with widening of the offshore cell.

The reef slope, without significant interference in the strength or velocity profile shape, also affects the zonation of SAG circulation cells, with steeper slopes providing wider SAG offshore circulation cells.

The groove width, the differential roughness between spur and groove, and the reef flat widths were shown to have a minor role in the SAG hydrodynamics.

The alongshore forcing leads to an alongshore transport system. The degree of the alongshore dominance is directionally proportional to the alongshore forcing. In the cross-shore direction, the onshore SAG circulation cell was persistent, while the offshore cell can be undermined with large alongshore forcing.

Long waves were shown to result in negligible influence in the mean SAG hydrodynamics, associated with the low long wave forcing observed in the SAG zone. They are primarily more important as approaching and within the reef flat, and the water exchange between this and the SAG zones was concluded to have limited influence in the SAG flow.

In terms of coral growth and health, bottom shear stresses were found to be systematically higher over spurs than grooves, resulting in a higher potential for coral development over them due to increasing water motion. Accordingly, sediment transport potential is higher over spurs, for which alongshore currents are higher than grooves, thus sediments would tend to drift towards the grooves, where they would more likely deposit due to lower shear stresses. The fact that SAG with distinct shapes - with significant different peak spur height depths - experience similar bottom shear stresses suggests the existence of a range of ideal hydrodynamics conditions for coral development.