Freshwater ecosystems are one of the most threatened habitats on earth. Freshwater vertebrates are majorly represented by freshwater fishes (69%) and amphibians (24%). Geographically isolated freshwater species such as those inhabiting islands, are particularly vulnerable to threats. Australia, having more than 9200 islands, is home to diverse island freshwater fauna. The lack of published literature on their occurrences, threats, and management impedes effective conservation. Our study summarized our current knowledge by developing the Occurrences of Freshwater Fishes and Frogs of Australian Islands Database (OFFFAI). Utilizing OFFFAI, we analyzed the drivers of distributional pattern, species richness, and species composition on Australia’s island freshwater ecosystems. The OFFFAI database cataloged 96 freshwater fishes and 104 amphibian species. 58 fishes were obligate freshwater species, 20 were euryhaline and 18 were diadromous. We found that amphibian and freshwater fish richness were positively correlated to island area. Larger islands likely had larger and more diverse habitat which supports more species. Amphibian richness was negatively correlated with distance from mainland, as closer islands likely retained mainland amphibian assemblages. The influence of distance from the mainland on fish richness appears to be not significant, potentially due to euryhaline and diadromous fishes being able to disperse through marine habitats.