Strong relationships between seasonal flooding, instream habitat structure and fish assemblages have been well documented in large tropical rivers (e.g. the flood pulse concept). However, the mechanics of these relationships are likely to differ substantially in smaller coastal rivers, such as those in Costa Rica, south-east Brazil and Australia’s Wet Tropics. These systems typically feature steep upland streams with short, deeply incised lowland channels and poorly connected floodplains. This hypothesis was investigated by documenting spatial and temporal variation in fish-habitat relationships in the Mulgrave River, north-east Queensland. Sampling was conducted at four lowland sites under a range of flow conditions, from dry-season baseflows to a one-in-ten-year flood. Longitudinal environmental gradients and fine-scale habitat patches were important in regulating fish assemblage structure during the dry season. However, high wet-season flows, constrained by the deep channel, acted as disturbances rather than gentle flood-pulses. In particular, the mobilisation of bed sediments led to scouring of aquatic vegetation and a dramatic reduction in habitat heterogeneity. Seasonal movements of fish led to significant changes in assemblage structure – from a community dominated by Neosilurus ater, Hypseleotris compressa, Awaous acritosus and Redigobius bikolanus during the dry season, to one dominated by Nematalosa erebi, Ambassis agrammus and Glossamia aprion during the wet season. Based on these observations, together with information from the literature, a conceptual model of fish-habitat dynamics is presented that is better suited to small tropical rivers than those developed in larger systems with expansive floodplains.