Estuaries are among the most productive ecosystems per unit area, but this productivity is unevenly distributed across a complex mosaic of habitats. Identifying the qualities of different habitats that influence the composition and productivity of biotic communities is fundamental to understanding the dynamics of these ecosystems. We combined field surveys, hydrological modelling and stable isotope analysis to understand the roles of habitat, hydrological connectivity, salinity and temperature in determining assemblage composition, species abundance and trophic ecology of an estuarine fish community. Hydrodynamics, vegetation matrices of macroalgae and seagrass and the presence of epiphytes on vegetation explained spatial patterns in taxonomic biodiversity, multivariate assemblage structure and the occurrence of juvenile black bream Acanthopagrus butcheri, a species that possesses ecological traits common to many demersal estuarine fish species. Juvenile bream abundance was related to vegetation composition (particularly epiphyte presence), supporting the hypothesis that juvenile habitats that provided resources or conditions that extended beyond just structure conferred more ecological advantages. This was further evidenced by stable isotope-based estimates of basal resource contributions of epiphytes. Our findings suggest that hydrodynamic connectivity with riverine water masses acts as a coarse determinant for estuarine fish communities at large spatial scales. At smaller scales, habitat-level associations influence local abundances and the identity and importance of specific trophic resources. Coupling hydrodynamic modelling with natural biomarkers provides a powerful approach for assessing the spatial context of habitat use that can help resource managers prioritize monitoring and habitat preservation efforts for coastal fish communities in a changing global environment.