Black mudfish (Neochanna diversus) were found at 39 of 80 sites in the Waikato region, New Zealand, ranging from large wetlands to small swampy streams. Of the sites with mudfish, 87% were dry at some time during summer. Sites with mudfish also generally had emergent and overhanging vegetation and tree roots, and showed low to moderate human impact. Black mudfish coexisted at some sites with juvenile eels or mosquitofish, but were absent from all sites with common bullies (Gobiomorphus cotidianus) or inanga (Galaxias maculatus). Sites with mudfish had almost exclusively semi‐mineralised substrates or peat; only one site had mineralised substrate. Geometric mean catch rate for the 39 sites with mudfish was 0.70 fish per trap per night. Mean summer water depth was only 2.1 cm at sites with mudfish, compared to 22.6 cm at 41 sites without. Winter and maximum water depths were also less at sites with mudfish than at sites without mudfish. Mean turbidity was 11.5 nephelometric turbidity units (NTU) at sites with mudfish, but 21.3 NTU at sites without mudfish. Mudfish catch rates were negatively correlated with summer water depth, winter water depth, disturbance scale rating, and turbidity. A discriminant function model based on these variables successfully predicted 95% of the sites with mudfish. Habitat preference curves are also presented.