A rise in the global mean temperature induced by climate change is expected to have a large impact on ecosystems in all regions of the world. One of the threats is accelerated sea level rise (SLR). This may induce the loss of intertidal areas in tidal inlet systems. The long-term morphological response of tidal inlet systems can be modelled using reduced complexity model ASMITA (Aggregated Scale Morphological Interaction between Tidal inlets and the Adjacent coast). The ASMITA model simulates morphological development on an aggregated spatial and temporal scale by imposing a morphological equilibrium condition. As such the model is fast, allowing for multiple long-term simulations. The model is physics-based and the parameters can be related to field values.

Currently, salt marshes are not implemented in ASMITA. However, salt marshes could be of importance to the morphological development in tidal inlet systems. Moreover, it is relevant to assess the resilience of the ecologically important salt marshes by themselves. The aim of this research is to implement salt marshes in ASMITA to assess their influence on the rest of the tidal inlet system and to gain insight into the long-term morphological response of salt marshes to accelerated SLR.

Salt marsh development is governed by horizontal and vertical processes. The marsh height increases by capturing mineral sediment and by the accumulation of plant biomass. Autocompaction and deep subsidence lead to a decrease in marsh height. The implementation of salt marshes in ASMITA relies solely on the input of mineral sediment. At the marsh edge, generally, a cyclic behaviour of sedimentation and cliff erosion occurs. Due to the high degree of spatial aggregation, cliff erosion is excluded from the model extension. The governing processes for salt marsh development in the ASMITA model extension are mineral sedimentation, sediment availability and relative SLR.

The spatial and temporal aggregation of governing processes for salt marsh development are included in the aggregated advection-diffusion equation and model parameters for the horizontal & vertical exchange of sediment, and sediment availability. Data analysis on hydrodynamic conditions and salt marsh development was conducted for the derivation and calibration of these model parameters. To verify the salt marsh implementation, three ASMITA models were created. A one-element salt marsh model consisting of only a salt marsh element, and two different multiple elements models, which contain the ebb-tidal delta, channels, tidal flats and salt marshes.

It can be concluded that ASMITA can model the mineral sedimentation on a salt marsh but depicts a large sensitivity to the parameter setting, particularly for the sediment concentration. Based on the chosen parameter configuration, the Oosterkwelder salt marsh is preserved when subjected to SLR rates below 16 mm/year.

The ASMITA salt marsh extension can be employed to obtain an expeditious first impression of long-term morphological salt marsh development. However, due to the lack of incorporation of detailed processes, the model should not be employed for in-depth analyses of salt marsh development. The interaction between the salt marsh element and the remaining tidal inlet system components requires further model improvements.

KEY POINTS (I) A biophysical model framework (BMF) for corals is developed in which four environmental factors are included: (1) light; (2) hydrodynamics; (3) temperature; and (4) acidity. (II) The full feedback loop between corals and their environment forms the core of this model framework, where the morphological development is new and closes the feedback loop. (III) The developed BMF predicts the coral response to environmental input via (mainly) process-based relations within the accuracy of climate projections. (IV)- The BMF supports both the deep reef refugia hypothesis and the turbid reef refugia hypothesis. (V) The BMF contributes to the development of protection and recovery programs and is not site-specific. (VI) The BMF is developed for long-term predictions - in the order of decades to centuries - but runs on daily averages and is therefore applicable for assessing the response of corals on shorter time-scales; such as months to years. SUMMARY The increasing pressure on Earth’s ecosystems due to climate change becomes more and more evident. These pressures are especially visible at coral reefs. Therefore, a good understanding of the biophysical mechanisms controlling these ecosystems is needed, so that accurate predictions of their survival can be made. Such an understanding is also needed to develop efficient recovery and protection programs vital to the maintenance of these ecosystems. Because the research on marine ecosystems is relatively young and the phenomenon of coral bleaching is yet to be fully understood, there is no comprehensive framework in which the complex interactions between corals and their environment are combined. In this study, a biophysical model is developed in which four environmental factors are included in a feedback loop with the coral’s biology: (1) light; (2) hydrodynamics; (3) temperature; and (4) acidity. Literature from multiple disciplines is combined to find the interdependencies between the corals and their environment. These relations include coral growth, coral bleaching, storm damage, and recruitment/recolonization of corals. For the connection with the hydrodynamics, a coupling is made between the biological model developed here and Delft3D-FM. The composed biophysical model is a big leap forward in understanding the world of coral reefs, as it is the first construction of a model framework including four environmental factors in which the hydrodynamics are included in the feedback loop. Furthermore, it creates the ability to assess recovery and protection programs based on the four aforementioned environmental factors; e.g. the susceptibility of coral bleaching can be reduced by increasing the attenuation of light through the water column. Because more environmental factors have a role to play in the coral dynamics, the framework is constructed such that these can be added relatively easily.

Seagrass meadows are essential and valuable to many shallow coastal ecosystems, due to the many important ecosystem services they provide. The interaction of feedbacks between hydrodynamics, sediment dynamics, and eelgrass can be described with a feedback loop. At locations where eelgrass is present, it favours its growth by modifying the local hydrodynamics (both waves and currents) and the sediment transport. Sediment resuspension is reduced by eelgrass presence, the light availability is subsequently increased, and growth is stimulated, i.e. further reducing the sediment resuspension. However, when eelgrass is absent, its growth is adversely affected. Sediment resuspension and, therefore, turbidity is enhanced, the available light is reduced, and eelgrass growth (or invasion) is hindered. Therefore, these systems are vulnerable and prone to external factors that influence the environmental conditions to become adverse. Especially hindered light penetration or changes in water temperature can push the system to an alternative ecological state, i.e. from dense eelgrass cover to a bare sediment state, with a little chance of return. Climate change effects, such as sea level rise, water temperature increase, and increased storminess, can increase these threats to the seagrass ecosystem and are, according to the literature, able to push the ecosystem into the bare seabed state. Because of its vulnerability and valuable benefits, conservation of and prevention of damage to the ecosystem are strongly demanded. To this end, the shallow coastal (eco)system response to possible adverse conditions of a changing environment due to the mentioned climate change effects is assessed in this research. The Rødsand lagoon in Denmark was found to be an ideal study site, as it is characterised as a sheltered, shallow microtidal coastal system that accommodates eelgrass and that has been intact for many years. It is a good example of a thriving eelgrass ecosystem in a temperate climate, and a low-nutrient environment, where anthropogenic influences are limited. The environmental conditions of the study site could be assessed by means of the available literature and the data that was provided. In general, the hydrodynamic conditions are primarily dependent on wind, as this is the main forcing of both flow and waves. The flow- and wave conditions are, in general, relatively calm, which means that only for dynamic (storm) events sediment resuspension is induced. In order to assess the interaction of feedbacks between hydrodynamics, sediment dynamics, and eelgrass, and the impact of climate change effects on the coastal system, a predictive tool in terms of a numerical model that includes these feedbacks was developed. This resulted in the coupled model: an interactive coupling between a physical model and a growth model was established. The physical model, developed as an online coupling of Delft3D-FLOW with Delft3D-WAVE, includes the effects of flow and waves on the sediment entrainment and therefore on the vegetation. The growth model simulates the eelgrass development over time based on the environmental conditions computed by the physical model and the subsequently calculated light climate. The simulated eelgrass development by the growth model was subsequently used as an input for the physical model for the next simulation period. The developed coupled model was used as a predictive and pragmatic tool: simulations comprising idealised singular climate change effects of relative sea level rise, water temperature increase, and increased storminess were performed. The results of the coupled model and the provided data of DHI showed the same behaviour in terms of eelgrass development, hydrodynamic conditions, and sediment transport at most locations, except in the deepest depth zone (4-6 m). This indicates that the general performance of the coupled model is adequate. The environmental conditions in the coupled model are apparently more benign than in the model of DHI, i.e. more beneficial for the eelgrass growth, as the eelgrass biomass was far higher at the shallow depths than that the data of DHI showed. Two reasons can be given for these more beneficial conditions: 1) the sediment import from the offshore boundary and spreading into the domain is underestimated, resulting in more beneficial light conditions at the bottom and 2) the model only takes into account the forcings and, therefore, the hydrodynamic processes in the direction of the transect, whereas processes (related to hydrodynamics and sediment transport) acting perpendicular to the transect are omitted. The results showed the impact of these climate change effects on the coastal system, especially on the eelgrass development. Decreased growth could be observed for all simulated climate change effects compared to the results of the baseline case with dense eelgrass cover. As the eelgrass at the deepest locations is the closest to its light-/depth-limit, it was found to be more susceptible to changes in the environment than eelgrass at shallower locations, leading to increased decay at larger depths. However, no indication or no clearly defined threshold of the system shifting to the alternate and undesired bare state due to the studied climate change forcings, i.e. relative sea level rise, water temperature increase, and increased storminess, could be derived for this specific study site. This means that a large-scale die-off of eelgrass in a shallow microtidal coastal system such as the Rødsand lagoon is unlikely to happen due to the studied forcings.

Global flood exposure simulations show that about 600 million people, of which 320 million in urban areas, are at risk to the impacts of global sea-level rise and changing storm intensity and frequency. Increasing availability of data and computational efficiency enables to assess flood hazard on a global scale. Implementation of salt marshes and mangroves as nature based flood defences has gained strong interest in the field of hydraulic engineering during the last decade, because these ecosystems can be an innovative, sustainable and cost-effective supplement to manmade traditional coastal protection measures. This thesis focuses on wave damping by salt marshes and mangroves and aims to map flood hazard reduction by foreshore vegetation on a global scale.

Wave attenuation by foreshore vegetation is accessed using transects which are aligned perpendicular to the Open Street Map (OSM) coastline. The study area contains in total 495361 transects, which have an intermediate distance of roughly 1 km and are individually assessed. The assessment of each transect involves construction of the foreshore profile, derivation of vegetation presence and the corresponding vegetation type, determination of the governing hydrodynamic conditions and computation of wave propagation over the foreshore. Wave damping by foreshore vegetation is determined by comparing the wave height at the end of the vegetated zone with a bare foreshore situation. The analysis is based on topobathymetric data from the Global Interidal Elevation map (20 – 30 m resolution, 1 m vertical accuracy) and a merged set of MERIT elevation data (3 arc-seconds resolution, 2 m vertical accuracy) and GEBCO bathymetry data (30 arc-seconds resolution, 10 m vertical accuracy). Vegetation presence is based on the VegGEE map (resolution 10 -30 m) and the cover type is based on the Salt marsh map, Mangroves, GlobCover or CLC. Wave characteristics are derived from ERA-Interim reanalysis and extreme levels from the Global Tide and Surge Model (GTSM). The nearshore wave height is based on a depth limited criterion and wave propagation over the derived foreshore is determined using a dataset of XBeach pre-runs.

The results of the global assessment show that 31% of the coastline in the study area (between the Arctic circle and -60 degrees South), is vegetated, of which more than half has a vegetation width that is larger than 100 m and 5% has a vegetation width exceeding 1000 m. Along 5% (15%) of the studied (vegetated) coastline is a significant wave height reduction observed of at least 30 centimetres. The performed global flood hazard reduction assessment is unique, as it uses global open source data to express quantitatively wave damping by salt marshes and mangroves on a global scale. The results show the effect of foreshore vegetation in terms of wave attenuation, reduced dike height and the potential social impact. Based on the performed analysis can be concluded that foreshore vegetation has a high potential to mitigate flood hazard at various areas around the globe.