Amphibians are more threatened than any other vertebrate class, yet evidence for many threats is missing. The Cape lowland fynbos (endemic scrub biome) is threatened by habitat loss, and natural temporary freshwater habitats are removed in favour of permanent impoundments. In this study, we determine amphibian assemblages across different freshwater habitat types with special attention to the presence of invasive fish. We find that anuran communities differ primarily by habitat type, with permanent water habitats having more widespread taxa, while temporary water bodies have more range restricted taxa. Invasive fish are found to have a significant impact on frogs with toads most tolerant of their presence. Temporary freshwater habitats are a conservation priority in the area, and their amphibian assemblages represent endemic taxa that are intolerant of invasive fish. Conservation of a biodiverse amphibian assemblage in lowland fynbos areas will rely on the creation of temporary freshwater habitats, rather than a northern hemisphere pond based solution.