Coral reefs play a crucial role in coastal protection and ecosystem sustainability. However, they face increasing threats from sea-level rise, ocean warming, and acidification. While coral reef restoration is often proposed as a means to reduce coastal hazards, there remains insufficient field evidence or large-scale laboratory data to validate this claim. A key aspect in assessing the effectiveness of reef restoration is understanding the flow structure within artificial reefs, as wave energy dissipation is closely tied to these dynamics. Not accounting for in-canopy flow in numerical models can lead to inaccuracies in predicting wave dissipation and water level changes.

This thesis investigates wave transformation and dissipation through large-scale wave flume experiments conducted at Deltares' Delta Flume. The experiments utilized a 1:3 scale model of a Maldivian fringing reef, tested under five wave conditions and two water levels. The experimental setup included a 45-meter-wide reef flat, where a 10-meter section was equipped with either 91 or 153 3D-printed artificial reef elements (0.25m high, 0.40m wide). Data were collected using pressure sensors and flow meters to measure wave transformation, while two ADV arrays analyzed in-canopy flow. These CREST experiments, carried out in collaboration with Plymouth University, Deltares, Boskalis, and Coastruction, contribute to the ARISE project, which explores atoll island adaptation to rising sea levels.

The research addresses four primary objectives: (a) evaluating the impact of artificial reefs on wave transformation, frequency dependence, and water level response; (b) identifying in-canopy flow characteristics; (c) linking these flow characteristics to wave dissipation; and (d) assessing the accuracy of an existing in-canopy flow model.

Findings indicate that as water levels rise, the relative height of the artificial reef decreases, leading to a decline in wave height reduction capacity. The reduction ranges from 8.5% to 15.2% at low water levels and from 4.9% to 5.9% at high water levels. Despite reducing incoming wave heights, artificial reefs can, under certain conditions, increase rather than decrease extreme water levels onshore due to the artificial reef-induced drag force amplifying wave setup.

Analysis of streamwise velocity variance revealed significant spatial differences. Velocity variance decreased more in the ADV array located behind the reef elements compared to the ADV array positioned between them, where velocity variance increased. Flow attenuation was found to be more pronounced at lower water levels, with longer and higher waves attenuated more effectively than shorter and lower waves. The modeled canopy wave dissipation rate, was found to be 43-87% lower than observed dissipation, though still within the same order of magnitude. The discrepancy is partly due to the model not accounting for breaker dissipation and non-linear energy transfers. Flow convergence corrections significantly increased flow attenuation and reduced canopy dissipation rates, while ADV selection had minimal impact.

According to canopy flow regime classification, the tested conditions fell between inertia-dominated and general flow. Reducing element spacing could shift the flow further into the general flow regime, enhancing frequency dependence in flow attenuation and wave dissipation. Given its limited wave height reduction capacity, artificial reefs like these would be most effective when integrated into hybrid coastal protection strategies. Such combinations could enhance both coastal resilience and ecological benefits. Ultimately, the CREST experiments provide a valuable dataset for model calibration and validation, contributing to a deeper understanding of reef hydrodynamics and in-canopy flow dynamics.

Over 30% of the world's coastline consists of permafrost and large sections of these coasts are subject to erosion. In the Arctic, unlike with temperate low-latitude coastlines, thermal processes affect erosion mechanisms. There is a lack of long-term predictive capability of morphodynamics for Arctic coastlines, which results in a knowledge gap regarding the coastal processes inducing permafrost erosion and how these processes will change under the effects of climate change. Previously developed parametric morphodynamic permafrost models lack generalizability because they either do not include all erosion mechanisms or were calibrated for specific eroding coastlines. Comprehensive morphodynamic models that include permafrost dynamics are too computationally expensive to perform long-term analysis and are thus applied to storm time scales only.

This study implements a novel method that integrates thermodynamics, hydrodynamics, and morphodynamics to predict the morphodynamic evolution of a permafrost-affected coastline. We developed and validated a process-based numerical model for Barter Island (North Slope, Alaska). This model showed skill in predicting the ground temperature distribution and the erosion of a permafrost bluff. Sensitivity analyses indicated that the environmental drivers affected by climate change (i.e., air and sea temperatures, water level) are expected to accelerate the erosion of permafrost-affected coastlines under the effects of climate change, confirming the findings of previous work. Rising temperatures will compound with diminishing sea ice to widen the annual window during which erosion can occur, which will increase the number of storm events that lead to erosion. Lower bluffs composed of finer sands are especially vulnerable.

The low computation costs mean that the model can be used to predict coastal erosion for larger regions, potentially benefiting strategic coastal management and policy-making.
Additionally, the developed model will improve global climate models. It can facilitate the mapping of permafrost degradation and organic carbon release, with the release of organic carbon through permafrost erosion being one of the greatest unknown drivers of global warming. Though further calibration is required, the developed model can be used as a tool to research the quantitative effects of climate change on the erosion of Arctic coastlines and gain a deeper understanding of how climate change affects the processes that ultimately lead to the erosion of permafrost bluffs.

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.

The present thesis describes the development of a hybrid behavioural / process-based and wave-averaged model (XBeach Surfbeat) that successfully predicts the recovery of the subaerial beach at Narrabeen Beach, Australia, following a severe storm erosion in April 2015. Two model innovations were developed. Firstly, a behavioural model was developed to predict berm growth during calm conditions, as well as erosion during episodic storm conditions. A second innovation calculates a re-distribution of the sediment transport in the upper swash zone, to account for incident band swash-induced sediment transport, which is not resolved in XBeach Surfbeat, but is of major importance, especially on reflective beaches. The model successfully predicts the behaviour of the beach throughout the recovery period, and shows good potential for long-term simulations.

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.