Mangrove forests are important (sub)tropical intertidal ecosystems providing coastal protection and other ecosystem services like carbon storage and biodiversity. In view of the loss of these forests many rehabilitation projects have started, but unfortunately these efforts often fail. A main cause for coastal erosion is a disrupted (fine) sediment balance due to human interventions. This imbalance prevents establishment of propagules (floating mangrove seeds) at intertidal areas and the early growth of planted mangroves. Coastal solutions such as permeable dams have aimed to stop the erosion, but we need additional systematic methodologies to understand the coastal system.

The objective of this thesis is to extend the physical and ecological understanding of coastal mangrove systems, especially of currents, sediment pathways and propagule pathways, to improve rehabilitation strategies using Demak (Central Java, Indonesia) as study area. Demak's coastline suffers from erosion problems, originating from extensive land use by fish ponds and land subsidence. An idealized morphostatic 3D model was set up in Delft3D-4 to simulate the hydrodynamics of the area, influenced by the interaction between flows due to river discharge, tides and wind. The simulations are used as input for the SedTRAILS particle tracking model to compute sediment and propagule pathways.

The model results support that sediment supplied by alongshore currents and riverine sediment could serve as source for the coastline. The river plume is at the same time obstructing as well as trapping sediment and propagules, because stratification prevents mixing of the sea and river water. However, sediments suspended near the bed could be transported underneath the river plume towards the coast by estuarine circulation. Another lesson learnt is that sediment (suspended in the water column) and propagules (floating around the water surface) do not follow the same pathways, as for propagule dispersal the wind direction is of much larger influence than tidal currents. The simulations confirmed that seasonal variability in wind direction could significantly influence the establishment area and availability of propagules, and old fish pond bunds can increase the establishment area for propagules. Sensitivity analysis show that the timing of propagule release within one tidal cycle (flood-ebb) influences the probability to successfully establish on the nearby coast. A propagule survival module is developed (based on inundation-free period and bed shear stress) as stormy seasons may increase the sediment establishment, but the larger bed shear stresses may lower the survival of propagules.

Although this modelling study is focusing on Demak, there are many other similar mangrove coasts around the world where an idealized model would enable to understand where the sediment and propagules are going and the travel time from source to sink. Permeable bamboo dams would be recommended to add to the model in further research, because they could increase the survival of propagules by reducing bed shear stresses and increase the establishment of propagules by trapping them. In conclusion, this research has made a start in counteracting coastal erosion and improving the success of mangrove forest rehabilitation by studying sediment and propagule pathways, and developing a propagule survival module.

Mangrove forests are important wetland ecosystems that inhabit intertidal zones within tropical and sub-tropical latitudes. They offer a diverse array of ecosystem services, including coastal protection and carbon sequestration. Despite their significance, global mangrove cover has declined in recent decades, prompting various restoration initiatives, most of which often fail due to a lack of system understanding of the local mangrove habitat and associated physical and biological processes. A method gaining prominence involves the use of permeable dams to restore the sediment balance along eroding coastlines, thereby facilitating the restoration of mangroves in the area. These dams help dissipate the approaching waves and reduce current magnitudes, thus creating a low energy environment behind them, ideal for sediment deposition. However, a comprehensive understanding of the system-wide implications of utilisation of permeable dams remains largely unexplored.

The study is focused on examining the response of a coastal system to structural presence, based on currents, waves and sediment and propagule pathways, to optimise restoration strategies. The coastline of Demak in Indonesia is chosen as the system to be modelled due to the persistent erosion problem in the region and the ongoing use of permeable and impermeable structures to mitigate the problem. A nested model was set-up in Delft3D-4 to estimate the flow hydrodynamics resulting from river discharge, tide and wind forcing in the area. Wave propagation in the region was also modelled using Delft3D-4 with a standalone nested wave model. Output from the hydrodynamic models served as input for the Lagrangian particle tracking model, SedTRAILS, to compute the sediment and propagule pathways.

The hydrodynamic models demonstrate a decrease in both current magnitude and wave activity behind the structures, with a greater reduction observed in the case of impermeable structures. However, the radius of influence is constrained to less than a kilometre from the structures. The sediment pathways reveal reduced sediment movement behind the structures. However, the sediment imported due to the structures are sourced from within the intertidal basin which could trigger coastline retreat in the region. Additional tests uncover impermeable structures with larger length to opening size ratio, placed closer to the mangrove fringe to be able to retain sediment with comparatively higher efficiency. In case of propagules, the trapping behaviour of the structures is less apparent, with dependencies on the relative location of the structure to the sources and the direction of wind. In Demak, when structures are located relatively offshore to the propagule sources, they are able to trap the propagules, thereby creating a possibility for mangrove restoration. The study concludes that coastal structures enhance sediment and propagule retention, with varying efficacy depending on the type, location and length of the structure, suggesting their potential utility as a valuable tool for mangrove restoration.

To estimate wave attenuation by mangrove forests, trees are often schematized as uniform cylinders (over the height) representing a tree’s stem. However, trees have more complex geometrical features that influence the interaction between waves and tree structures. Recent studies have shown that the frontal surface area distribution over the height Av(z) is a crucial parameter for estimating wave attenuation by vegetation (Kalloe et al., 2022; van Wesenbeeck et al., 2022) because it can account for complex geometrical features. This study aims to model the complex geometry of the Avicennia marina mangrove species. The research question then becomes:

How to construct geometrical tree models of Avicennia marina vegetation and how to obtain the projected frontal surface area distribution over the height, Av(z)?

In this study, manual measurements were performed to obtain tree structure parameters. Both canopy and root measurements were conducted for Avicennia marina vegetation with varying characteristics (age and density). Two saplings (approximately 1.5 years old) with variable canopy densities and two young trees (around five years old) with varying canopy densities were measured. We stored canopy measurements in a so-called tree data structure consisting of nodes (representing the branches) that contain information about the individual branches, such as branch orders, -lengths and -diameters and edges, which are links that establish direct relations from one branch to another. After that, we developed a search tree algorithm to loop through all tree data, compute parameters of interest and store the results in assigned data arrays. Parameters of interest to obtain after the data analysis were branch dimensions and diameter ratios of branches (between various branch classes). This information was necessary to create a blueprint for constructing geometrical tree models.
Tree modelling started with the construction of a root (pneumatophore) model. Additionally, the frontal surface area of these roots was computed and displayed as a function of the height. In addition to the root model, we constructed two canopy models. The first model is based on relations between branches and can be called deterministic or dependent (canopy model 1). The second canopy model (canopy model 2) generates branch dimensions based on the normal distribution of branch diameters and is, therefore, more probabilistic with branches independent of each other. Both canopy models construct branches based on information travelling from preceding branches. The models account for the proper placement of branches within 3D space by rotations and translations. The algorithm computes and outputs the projected frontal surface area over the height of a system of branches for a given direction (XZ-plane projection or YZ-plane projection). We validated the two canopy/tree models against validation measurements. Three trees were divided into seven vegetation layers, and branches were registered that intersected with the layers. As a result, estimation could be made on the frontal surface area per layer.

This study found that the frontal surface areas due to roots and canopies are significant and are well represented by the parameter Av(z). The contribution of the roots and canopy cannot be neglected in modelling wave dissipation by vegetation. The contribution of smaller branches to the total Av is significant, proving that considering only the tree stem is an underestimation. Moreover, the research shows that it is possible to develop a geometrical tree model based on a set of measurements and design rules that follow from observations, at least for the considered tree species. We could extrapolate and interpolate our results to generate tree models for a wide range of tree ages. Additionally, it is possible to create a forest by generating multiple trees.

Both tree models (1 and 2) showed little differences in Av(z) during the model validation process. Moreover, the validation measurements led, in general, to an overestimation of the total frontal surface area. Consequently, model validation was inconclusive regarding both tree models. However, we found that constructing tree models according to tree/canopy model 1 is preferred because it resembles an L-system more and is more practically applicable in computer models. We can improve future tree models by collecting more measurements regarding branch structures and root distribution as a function of tree age. This will result in increased model reliability.

Mangroves trap sediment and are the first coastal defence line for many coastal areas. Unfortunately, mangrove coasts worldwide are eroding due to deforestation, exposing local communities to flood hazards. In Demak, Indonesia, a Building with Nature approach was chosen to counteract erosion. Permeable dams were built on the foreshore to attenuate waves and restore the sediment balance. The dams have increased the bed level locally and mangroves expand after construction. A new project called MuMaCo (Mussels as Mangrove facilitators for Coastal defence) is launched to integrate mussel aquaculture into the mangrove rehabilitation project in Demak. Mussels increase the roughness and diameter of the bamboo poles, which could increase their wave attenuation capacity. Moreover, mussel culture gives the local communities an economic incentive to sustain the structures. This thesis describes and quantifies how mussels' growth influences the forces acting on bamboo poles. Small-scale experiments are performed in the wave flume of the Delft University of Technology on a scale of 1:3 and 1:6. Physical models were used for experiments with steady flow and waves. The steady flow experiments cover a range of Reynolds (Re) numbers between 10^3 and 10^4 to seek the drag crisis. Single mussel covered cylinders for both scales are compared to smooth cylinders and cylinders with an equivalent diameter. For the wave experiments, cnoidal waves with Keulegan-Carpenter ($KC$) numbers ranging from 3 to 113 that correspond with measured waves in Demak are chosen. Moreover, only mussel covered cylinders are compared to a smooth cylinder for a scale of 1:6. During the experiments, the flow velocity, force, and surface elevation are measured, and the drag and inertia coefficients are obtained with the help of the Morison equation. The drag coefficient shows a clear relationship with the Reynolds numbers for steady flow. Although the drag coefficients display the same qualitative behavior as in other studies in the literature, the drag coefficients of the smooth cylinder are more than 40 % larger than in the literature. This is probably due to large variations in the offset of the velocity meters (EMS) during the experiments. The large mussels show higher drag coefficients than the smooth cylinder. For the wave experiments, the drag coefficients show good correspondence to other studies in the literature, but the inertia coefficients are a factor two larger than expected for smooth cylinders. Treating the peak and trough of the cnoidal wave as individual sinusoidal waves shows similar results and suggest that cnoidal waves can be represented by KC numbers, as it is done for linear waves. The best fit to the literature values was found by solving the Morison equation with the measured force with the depth-integrated velocity squared and acceleration from the Fenton theory. This suggests that the results of the wave experiments have been uncertain due to inaccuracies in the EMS recordings. This thesis presents a method to schematize mussels for laboratory experiments and provides a qualitative comparison of the forces acting on poles with and without mussels

The coastline of Demak, Indonesia has been eroded during the last 15 years. To restore the natural coastal protection which existed out of mangroves forest, permeable dams, consisting of bamboo poles with a brushwood filling, have been built to attenuate the waves and facilitate sedimentation behind the dams and thus creating a habitat for mangroves. However these designs required a lot of maintenance, so a new type of design is proposed without a filling of brushwood, containing only vertical bamboo poles. Next to this the possibility to include aquaculture in the design is proposed. Therefore this study assesses the wave transformation by the new designs in Demak, Indonesia with the numerical wave model SWASH. In order to do that first the hydrodynamic conditions are analyzed to obtain the design conditions for the structures, and then SWASH is validated against laboratory experiments to find the right drag coefficient values. The design wave conditions are based on the local water depth, offshore wave heights and periods and local bathymetry. The offshore waves are based on a dataset from WaveWatch III, which compares well with measurements of a local storm event. The dataset of WaveWatch III is filtered and extrapolated to determine the wave conditions for return periods(R) of 1 and 5 years. This resulted in offshore waves with Hm0 = 2.08 and 2.39m, and Tp = 6.9 and 7.5 s respectively. The water level is mainly influenced by the tidal elevation and the surge levels. The surge levels are obtained from a risk assessment of the coast of North Java (Willemsen et al., 2019), which vary between 0.63 to 0.68mfor R = 1 and 5 years respectively. The tidal levels are determined using the water depth measurements of two transects from Van Domburg et al. (2018) and analysed with Matlab tool Utide by Codiga (2011), resulting in a spring tidal range of 85 cm and a neap tidal range of 50 cm.
Four different configurations from the experiments of Jansen (2019) are used to validate SWASH: single row, longitudinal(the spacing in flow direction is longer than the lateral spacing), open uniform and dense uniform configuration. These configurations are modelled in the numerical wave model SWASH by use of the vegetation module. The most influential factors are: the drag coefficient, the way to describe mass conservation and the number of stems(cylinders) per m2. For the drag coefficient the bulk drag coefficient of Gijon Mancheno et al. (2021) is used, which contains factors for sheltering, blockage and the KC state of the flow. For the densely packed configurations the bulk drag coefficient proved to have a better agreement than the drag coefficient of a single cylinder. The sensitivity to the number of stems per m2 is small when implementing the longitudinal configuration as an average amount of stems perm2 or by specifying the individual rows of the configuration and so locally increasing the number of stems. Three methods of describing the mass conservation in SWASH are evaluated: by means of a cross sectional approach that is expressed by the blockage factor in the bulk drag coefficient Gijon Mancheno et al. (2021), by a volumetric approach due to activating the porosity in SWASH which means that the blockage factor cannot be included in the drag coefficient and by a combination of these two. For the longitudinal configuration the best agreement is found the cross sectional approach and for the single row configuration the best agreement is found by the volumetric approach.
Once SWASH is validated, the designs of several structures are investigated. Firstly, a design consisting out of two rows of bamboo poles is considered where the spacing between the rows is varied to find an optimum distance. The transmission rate Et /Ei decreased from 75% to 55% with a spacing sx = 0.42 m to 5.8 m, larger spacings did not result in less transmission. If one wants to be conservative at least three rows are needed to have a lower transmission rate of 50 %. When mussels are considered, the structures have to be placed in deeper water as mussels can only grow between MLWS and 40 cm above the bed. To provide enough space for mussel growth, the poles have to be placed more sparsely. The effect of a larger water depth in combination with a limited pole length and sparse structures is larger than the extra drag and frontal area provided by mussels, especially since they did not cover the whole pole length, and resulted in high transmission rates. It is thus recommended to, or place a high number of rows of mussel poles or place a few rows without mussels followed by poles for mussels. This decision however also depends on benefits that mussel poles may bring and the cost of the materials, therefore a cost/benefit analysis is required.
This thesis found an efficient design that can be used in reducing wave attenuation along muddy coasts without the need of a brushwood filling. Hereby it provides an economically and user friendly alternative with respect to the current design, as it requires less material and maintenance.

The risk of flood risk is increasing with global trends such as rising sea levels, land subsidence, increasing populations in coastal areas and economic growth. Traditional solutions to reduce flood risk are a levee or a dam; however, the research on hydraulic engineering is increasingly promoting nature-based solutions for flood protection. Salt marshes and mangroves can attenuate waves and could thus help to reduce failure probability. This research focuses on the attractiveness of mangroves in flood risk reduction. The essence of the reasoning followed in this research is that mangroves in front of a levee enable a lower levee and therefore reduce costs while maintaining the same failure probability. There are three aspects related to this assessment: the biological behavior of mangroves; the physical behavior of waves and storm surge in a mangrove forest; and the economics of flood risk, levees, and mangroves. Mangroves grow under specific conditions, such as high temperatures, saline water with fresh water input, between mean sea level and high tide, and with low wave impact. Mangroves attenuate waves, with the attenuation rates depending on mangrove height, stem diameter and density, in addition to the water depth, wave height and wave period. Lastly, the costs of restoring mangroves and building levees have been considered. In this thesis a method has been developed to define the optimal configuration of a levee-mangrove system. The goal is to reach a desired safety level while keeping costs as low as possible. Costs consist of building a levee, restoring mangroves, and the expected annual damage and maintenance. This depends on the ratio of mangrove and levee costs, the ability of mangroves to attenuate waves, and levee characteristics. Although all variables have equal significance in defining the mangrove forest width, the variety in levee and mangrove costs and significant wave height are the variables most likely to affect the optimal mangrove forest width. Mangroves are only useful to decrease the height of waves, thereby reducing wave run-up. This wave-attenuating effect decreases exponentially with the mangrove forest width. all Based on the literature, when considering common values for levee costs and mangrove restoration costs, levee characteristics and wave attenuation, wave attenuation is strong enough such that the optimal mangrove forest width is larger than zero. The costs of restoring mangroves depend on the required measures to enable mangroves to grow back. Hydrological restoration involves returning the mangrove area to the natural condition where mangroves are able to grow. This could, for example, be restoring a fresh water source that has been blocked by human intervention. If hydrological restoration is required and can be done cheaply, then this is the most effective option. Planting mangroves can also be a cost-effective option. Sheltering the mangrove area by using a permeable structure requires more financial resources. If large-scale filling or excavation is required, costs may increase significantly, and it is likely to be too expensive to use mangroves in flood-risk reduction. However, this cost assessment may change if the ecosystem services of mangroves are taken into account. As a rule of thumb, for mangroves to be economically effective, restoration costs [USD/m/m] in case of a 1 m wave height should remain below 0.003 times the variable levee costs [USD/m/m]. This value increases linearly with the wave height. For levee costs of 1 million USD/km/m, of which 0.6 million USD/km/m variable costs, the mangroves restoration costs should not exceed 0.18 USD/m/m, or 18,000 USD/ha. For Kaback, Guinea, the optimal mangrove forest width and height of the levee are assessed. These are 900 meter and 1.1 meter respectively, with the levee located just behind the mangroves. 900 meter is the maximum width possible, considering the physical conditions where mangroves grow. Since mangroves are growing back naturally already, costs for mangroves restoration is limited to fixed costs. The model developed in this study can be used to create a ``mangrove opportunity map”. This map can indicate—based on physical attributes—the costs, hydraulic conditions such as storm surge and wave height, and whether mangrove restoration for flood risk reduction is effective. Governments or organizations such as the World Bank can use this method to explore whether mangrove-based strategies are an option. Further research can focus on improving the cost estimates on levees and mangroves. In this study, costs are assumed to be linear with the levee height or mangrove area. In practice, levee costs might especially increase exponentially with the levee height, which would make mangroves more effective.

In recent years, the interest in integrating shore protection with the local ecosystems has increased. In comparison with the traditional reinforced embankments, integrated shores form a gradual transition from land to water where shore vegetation can establish itself. These nature-friendly shores have a positive impact upon the water quality, flora and fauna and the amenities of the shore. Some of the benefits of vegetation are its capability of reducing the hydrodynamic loads on the shore and its ability to increase the soil strength against erosion. Both effects have been investigated in detail in previous research and have been implemented for coastal protection designs in sandy coastal settings. But a designing tool for cohesive shorelines in lake environments is still missing. In this research, the different aspects important for the erosion of a vegetated cohesive shoreline are studied and the first steps towards a process-based design tool are taken. The model results show that the dominant processes for erosion can be found at the point of wave breaking and at the start of the run-up, as both combinations give the highest induced bed shear stresses. This can be used for a strategic placement of vegetation to dampen the wave impact and reinforce the soil through the roots. There are situations in which a partially vegetated shore is sufficient to withstand the daily wave attack. This allows the vegetation to grow naturally to full strength, which is required in a storm situation. In this way a financial benefit can be reached as well as a healthier vegetated shore, as a large part of the vegetation has grown naturally.

Mangrove forests, which serve as a natural sea defence, have been degraded by human action during the last decades. To protect and recover these areas, different types of permeable structures consisting of bamboo have been proposed and applied. However, these structures are currently based on engineering judgement, as design rules are not available. The goal of this research is to make a step forward in the design optimization of permeable structures and gain a better understanding of the processes causing the wave dissipation inside the structure. In this study, scale experiments are conducted in the wave flume at Delft University of Technology. An array of aluminum cylinders is used as a schematization of the structure, with an element diameter of 4 cm and a minimum spacing of 2 cm. The tested wave height is 0.13 m,with a water depth of 0.6 m for the first set of experiments. These experiments evaluated wave transformation through a selected number of configurations. The water depth was 0.55 m for the second set, where the velocities and forces were also measured inside the structure. As the applied wave periods are short (T = 1 − 2 s), the tested wave conditions are in the range of small KC-numbers (4 < KC < 13). The first part of this research focuses on effect of different configurations and arrangements on the amount of energy dissipation, by measuring the incoming and reflected wave heights in front of and behind the structure. For the short waves, the horizontal arrangements dissipate more energy, as energy is dissipated by both the vertical and horizontal drag forces. However, the effect diminishes with increasing wave period. Considering the total dissipation and the amount of dissipation per element, the placement of the elements in rows perpendicular to the direction of wave propagation is found to be the most effective. To study the effect of the element diameter on the dissipation, the results are compared with previous research by Haage (2018) on a model with a diameter and spacing of 2 cm. As with the change in diameter also the structure porosity changed, a direct comparison was not possible and a comparison based on a simplified drag coefficient is done. No direct effect of the diameter is observed, as the obtained drag coefficients show the same trend and magnitude when plotted against an adapted Keulegan-Carpenter number (KC∗), which is based on the element spacing instead of diameter. Small KC∗-numbers result in large drag coefficients,which decrease when KC∗ increases. The second part of this research focuses on the processes inside the structure that cause the energy dissipation. A force and velocity sensor are applied at three locations inside the structure in separate experiments, to determine the relation of the force and velocity inside the structure with the undisturbed values. Two methods are applied for the analysis, based on two different principles. Method 1 is based on the assumption of a constant pair of force coefficients and an increase in velocity inside the structure, method 2 is based on the assumption of a constant velocity and an increase in force coefficients inside the structure.By comparing both methods, it is found that an increase in velocity is the most important factor for the increase in drag force, which is the driving factor for the energy dissipation. It is also found that the amplification factor for the velocity is dependent on both the structure porosity and frontal porosity.

Due to the removal of mangrove forests, coastal zones can suffer from severe erosion. One of the proposed solutions is the construction of permeable structures. This study aims to optimise the design of permeable (brushwood) structures in order to restore the sediment balance and encourage mangrove re-establishment on tropical mud coasts. Preferably wave transmission should be low in order to create a calmer climate behind the structure. In that way sediment is able to settle down, which could lead to a recovery of the mud profile. It is also preferred that reflection by the structure is low. High reflection rates cause scour holes that lead to instability of the structure. Furthermore, scour holes could hinder future mangrove re-establishment. Aiming to achieve low reflection and transmission rates, the dissipation inside the structure has to be as high as possible. Experiments were conducted in the 40 meter wave flume at the Environmental Fluid Mechanics Laboratory at TU Delft. The permeable structure was schematized as an array of cylinders. With the physical scale model various effects could be tested, including the porosity, structure width, arrangement, orientation, etc. The tests were done for 5 different wave cases, from which the wave energy distribution over reflection, dissipation and transmission was determined. The existing brushwood structures require intensive maintenance. This is partly due to the sinking of the material into the soft mud. Also, the brushwood material washes away often as it is lighter than water and difficult to constrain in vertical direction. An alternative design that requires less maintenance would be preferred. Therefore, it was interesting to see whether a comparable amount of wave dissipation could be achieved by using vertical elements only. One important finding is that in more shallow water regions, vertical and horizontal orientations have similar dissipation rates. In water regions that go more towards deep water, the horizontal structures have higher dissipation rates. This can be explained by the relative importance of the horizontal and vertical velocities due to the wave motion. In deep water vertical velocities are relatively high. As the horizontal elements have more exposure to this component in comparison to the vertical elements, they provide more dissipation. In shallow water the relative importance of the vertical velocities is lower, which explains the similar dissipation rates of the two orientations. The analytical model of Dalrymple (1984) was used to describe the energy dissipation through the structures. Drag coefficients were derived by using the calibration method. For KC<15 the drag coefficients start increasing. This is possibly due to the relative importance of the inertia force. Comparing the drag coefficients to the ones derived from direct force and velocity measurements in previous studies showed relative high values. This could be due to an underestimation of the horizontal velocity due to the wave motion. The velocity that is used is the undisturbed velocity in front of the structure. However, the velocity inside the structure might be higher as the flow accelerates in between the gaps of the elements. Furthermore, the wave cases in this research are in the Stokes 2nd and 3rd order region, indicating that the waves cannot be fully described by linear wave theory. The inertia, permeability and non-linear effects among other possible effects are not included in the analytical model of Dalrymple. Therefore, the drag coefficients do not only represent drag forces, but also other processes. To gain more insight on the physical mechanisms that affect the wave energy dissipation, it is recommended to test the same scale model with direct force and velocity measurements.