Understanding the relative influence of factors that influence faunal community structure, such as habitat and landscape arrangement, has been a long-standing goal of ecologists. This is complicated in marine environments by the high importance of physico-chemical water factors in determining species distributions relative to their physiological or behavioural limits. In this study, we rank the relative importance of 17 seascape, habitat and physico-chemical water factors for structuring the composition of fish communities on the inshore coral reefs of Moreton Bay, eastern Australia. Fish were surveyed at 12 reef sites along the ambient estuarine water gradient in the bay during summer and winter using a baited underwater video approach. Multivariate random forest analyses showed that reef fish community composition correlated most strongly with the local abundance of piscivorous fish and the seascape context of individual reefs (especially distance to nearest seagrass and mangroves), while water quality factors ranked much lower in importance. However, fish communities from sites nearer to rivers were more spatiotemporally variable than those from sites nearer to oceanic waters, indicating that water quality can drive variations in community structure along short-term temporal scales. In turn, piscivore abundance was greatest on reefs near large areas of seagrass, and with low sand cover, high coral cover and high water clarity. Our findings demonstrate that a reef’s location within the broader seascape can be more important for fish communities than factors relating to the reef habitat itself and exposure to reduced water quality. To improve the spatial conservation of marine ecosystems, we encourage a more intimate understanding of how these factors contribute to structuring the use of habitats across seascapes by mobile species.