Current and pervasive impacts of climate change and habitat loss threatens biodiversity. Species distribution patterns reflect those impacts throughout distribution shrinkage, expansions or extinctions. Wetlands are important and sometimes preferred habitats for many small-bodied fish species in the Murray Darling Basin (MDB). Wetlands are dynamic in spatial and temporal scales and can be subjected to different water regimes that impact their persistence and modify their environmental conditions. Our goal was to assess the role of large-scale factors, wetland specific environmental conditions, fish phylogenies, traits and residual cooccurrence patterns to understand distribution patterns in wetland associated small bodied fish species. To explore these processes, we analysed distribution patterns of 8 small-bodied and 4 exotic species in wetlands of 15 catchments in the Southern Murray Darling Basin (SMDB). All these variables were assembled in a Joint Species Distribution Models (JSDM) to obtain better resolution on patterns of variation that are associated with environmental, biological and phylogenetic traits and potential biological interactions. Our results indicated that fish responses to environmental drivers in wetlands are heterogeneous. In general species richness decreased with hydroregime, increased in larger wetlands and was negatively associated to temperature for native species. All exotic species, but Perca fluvailitis had positive responses to wetlands with higher temperatures. Catchment had similarly heterogenous effects indicating that many processes affecting small-body fish species are unique to each catchment. Residual cooccurrences revealed that native fish Galaxias rostratus, Hypsoeletris klunzingeri, and the exotic Cyprinus carpio, Gambusia holbrooki and Misgurnus anguilicaudatus have positive associations, yet the nature of the positive cooccurrence requires further testing. Altogether our results indicate that fish occurrences in wetlands are influenced by a combination of large scale and wetland specific factors with species interactions playing a significant role for most of the exotic species and some native small body fish species.