Urbanisation has transformed natural landscapes globally, having detrimental effects on the distribution of biodiversity and ecosystem functions in most biomes. But there are many properties of urbanisation, which shape populations and important processes in different ways. We do not know, however, whether different components of urbanisation exert separate or combined effects on assemblages and the distribution of functionally important species. We examined how the structural and nutrient properties of urbanisation influenced the composition of fish assemblages and the diversity of functional groups in estuaries of southeastern Australia. We surveyed fish assemblages across 22 estuaries that differed in their level of human modification, habitat diversity and water quality. Our results show the structural and nutrient properties of urbanisation affect fish assemblages, but they influenced different components of assemblages, and can interact. Estuaries with high shoreline urbanisation supported greater functional group diversity than relatively natural shores; characterised by a higher abundance of omnivores (e.g. yellowfin bream), zoobenthivores (e.g. weeping toadfish), and detritivores (e.g. sea mullet). Whereas, estuaries with higher nutrients displayed a greater abundance of zoobenthivores (e.g. common toadfish), which were functionally replaced by zooplanktivores (i.e. estuary perchlet) in lower nutrient settings. Landscape context influenced the effects of urban structure and nutrients on the functional composition of assemblages; for narrow estuaries, there was little influence of shoreline urban structure, nutrients or mangrove extent. This difference was characterised by a lack of zooplanktivores in larger estuaries. This suggests the functional effects of urban structures on assemblages is likely contingent both on the nutrient status and landscape context within which the structure sits. These findings have implications beyond estuaries, because urbanisation is widespread and influences assemblages in all ecosystem types. This has important consequences for monitoring the effects of urbanisation and how we might consider engineering ecosystems or restoring habitats that are moderately degraded.