Moreton Bay is a heterogeneous seascape containing a mosaic of habitats that support a diversity of fish. The fish fauna includes many species that are harvested by recreational and commercial fishers as well as numerous taxa that are of conservation concern. The fish fauna of mangroves, seagrasses, inshore reefs and intertidal flats is well sampled. By contrast, fish surveys in saltmarshes, soft sediments, offshore reefs and surf zones are sparse and incomplete. Fish diversity and abundance are typically highest on reefs and seagrass meadows, but most species move among habitats to feed and spawn. These movements connect habitats and link both fish assemblages and food webs across seascapes. The combined effects of water quality, coastal urbanisation and fishing also shape fish assemblages in Moreton Bay. Fish diversity and abundance increases from the urbanised western to the less developed eastern Bay. This spatial pattern mirrors gradients in water quality and habitat condition across the Bay. The shorelines of many estuaries and ocean beaches have been developed, and this coastal urbanisation has altered fish diversity, abundance and diet. Numerous species have, however, adapted to capitalise on the abundance of food and shelter in urban estuaries. No-take marine reserves prohibit fishing, and this promotes fish abundance and diversity in some ecosystems (e.g. coral reefs, seagrass meadows), but not in others (e.g. estuaries, ocean beaches). Important challenges for future research in Moreton Bay include: (i) testing how multiple human pressures combine to modify fish assemblages and fish habitats; (ii) identifying how the ecological attributes of ecosystems and seascapes shape conservation outcomes; and (iii) examining how fish assemblages, habitats and fisheries change in response to range shifts of tropical species that move south with rising sea temperatures.