Estuaries are important socio-ecological systems, often underpinned by the cooccurrence and functions of habitat-forming organisms. Endemic habitat-formers, including mangroves, oysters, and seagrass, can be indicators of healthy estuarine ecosystems by facilitating interactions and processes established over millennia. However, the introduction of non-native habitat-formers may alter the ecological communities and functions of these systems. Here, we assessed the effects of introduced, reef-forming Pacific oyster Magallana gigas, on a temperate mangrove-dominated estuary in Australia, investigating effects on intertidal fish and invertebrate communities, benthic structure, and foraging behaviour. Firstly, we characterised the structural traits and macrofaunal communities of bare sediment, mangrove Avicennia marina, and Pacific oyster-mangrove dominated habitats using photo- and extractive-quadrats. The fish communities associated with these habitats were then surveyed using unbaited remote underwater video stations and fyke nets. Pacific oyster aggregations showed no impacts on mangrove pneumatophore density or morphology, but facilitated higher sapling densities and enhanced invertebrate biodiversity. Similarly, the oyster-mangrove habitat supported greater fish species richness, higher counts of foraging behaviour, and larger small-bodied fishes, compared to the other habitats. However, several other non-native species including exotic Gobiidae and European green crabs Carcinus maenas, a declared noxious pest, were also facilitated by Pacific oyster aggregations. Overall, we demonstrated that Pacific oyster-mangrove habitats generally enhanced estuarine biodiversity, including fisheries-targeted species, but also facilitated other non-native species. These outcomes highlight some of the ecological pros and cons of non-native oyster reefs, and the complexity of managing estuarine systems where the co-occurrence of Pacific oysters and native habitat-formers is globally increasing.