Global climate change is a key driver of change in coastal waters with clear effects on biological communities and marine ecosystems. Human activities in combination with climate change exert a tremendous pressure on marine ecosystems and threaten their integrity, structure, and functioning. The protection of these ecosystems is a major target of the 14th United Nations sustainable development goal “Conserve and sustainably use the oceans, seas and marine resources for sustainable development.” However, due to the complexity of processes and interactions of stressors, the status assessment of ecosystems remains a challenge. Holistic food web models, including biological and environmental data, could provide a suitable basis to assess ecosystem health. Here, we review climate change impacts on different trophic levels of coastal ecosystems ranging from plankton to ecologically and economically important fish and shellfish species. Furthermore, we show different food web model approaches, their advantages and limitations. To effectively manage coastal ecosystems, we need both a detailed knowledge base of each trophic level and a holistic modeling approach for assessment and prediction of future scenarios on food web-scales. A new model approach with a seamless coupling of physical ocean models and food web models could provide a future tool for guiding ecosystem-based management.