The distribution and abundance of fish at sites in 38 medium to large New Zealand rivers were examined. Fish density varied from 5 to 200 fish per 100 m2, with an average of 53 fish. Our study sites contained a greater species richness and abundance than records stored on the New Zealand Freshwater Fish Database, where the average density was 28 fish per 100 m2. The average number of species at the study sites was 5, compared to 3 in the national database. Comparison of first‐pass catches with multiple‐pass population estimates showed that there was no difference in capture probability between species and that on average 51% of the population was captured on the first pass. The diadromous habit of many native species, and their ability to penetrate inland, was an overwhelming influence on their distribution. There was little regional variation in species composition, apart from the presence or absence of three non‐diadromous species. Two distinct fish communities were evident: lowland and upland. Lowland communities typically contained the highest density and diversity offish, whereas upland communities were dominated by one or two species. Many river sites were intermediate between lowland and upland, both in species composition and fish density, and showed a gradual reduction in abundance and change in community structure with elevation, as those fish less able to penetrate inland disappeared and non‐diadromous species began to appear. Elevation was the most important discriminating factor, with physical habitat and catchment variables less important. Fish densities were highest in gravel substrate of 50 mm or finer, and the amount of run and pool habitat may have influenced species composition. The relationships between catchment variables and species distribution and abundance were probably a reflection of geographical location.