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.