The freshwater shrimp Paratya australiensis is often found in urbanised streams north and west of Melbourne, however, it is rare or absent from similarly disturbed streams south and east of the city. We wanted to know whether this difference was due to biological differences among populations of P. australiensis, or an effect of physiographic variation across the region. We applied phylogeographic distributions of P. australiensis in Melbourne to long-term presence absence records (from both urban and non-urban streams). We then assessed the relative plausibility of five generalised linear mixed effects models (GLMMs) for predicting the occurrence of P. australiensis, in each region, that included effective imperviousness (EI) and four physiographic variables. We found that the two lineages of P. australiensis responded similarly to the effects of stormwater drainage (as indicated by EI). Thus, differences in occurrence of P. australiensis were related to physiographic variation rather than biological difference between lineages.