Habitat is rarely included in the models that we use to manage fisheries and ensure sustainability. Yet in shallow coastal ecosystems common fisheries targets associate with complex benthic habitats for some or all their lives. Habitats offer food, refuges, and recruitment sites, the provision of which are often dependent on habitat quality. Numerous stressors including global climate change, coastal development, and pollution are impacting coastal habitats, altering their structure and function with knock-on effects for the communities and fisheries they support. Understanding how coastal fisheries might change into the future, and ensuring continued sustainability requires us to effectively capture and quantify the impacts of habitat change on fisheries productivity and sustainability. In this talk I discuss how habitat can alter fish size structure, energy flows and fisheries productivity, and how, using size-based ecosystem modelling we have attempted to capture and value its role for coastal fisheries in both tropical and temperate ecosystems.