The distribution of fish in the urban gully system streams of Hamilton City was investigated using various methods of fishing. Fishing methods used in the city wide survey included trap netting using Gee minnow and fyke nets, electric fishing, and spotlighting at selected sites. Water quality and habitat parameters were assessed at each of the sites to add information to instream freshwater fish assemblages (i.e., preferred habitat). Culverts were assessed downstream of all sites because, native freshwater fish of New Zealand are largely migratory, having both freshwater and marine life histories. Freshwater fish migrate between habitats, therefore barriers to swimming fish passage may determine the presence of fish species at inland sites. Pest fish were less common than native fish in this survey, although they represent a greater proportion of the fish caught, because the small pest fish mosquitofish are prolific breeders and were present in very high numbers at a few sites. This study has shown that some urban streams can support diverse fish assemblages where water quality and habitat conditions permit. Threatened species were found to be present in streams previously thought of as supporting little stream life with low fish habitat or biodiversity value. The need for restoration and management of these streams is vital if the diversity and distribution of native fish is to be maintained.