An index of biotic integrity (IBI) was developed for freshwater fish in New Zealand streams. Data on freshwater fish occurrence for 5497 sites over the entire country were obtained from the New Zealand freshwater fish database for the period 1980–2002. Environmental habitat descriptors for the stream watersheds above or at each of these sites were obtained from an existing river environment classification using a geographic information system. Of the many IBI metrics in use globally, only six were adapted and applied because of differences between the fish faunas of New Zealand and the United States. A number of evaluation methods showed that all six metrics contributed to the overall IBI scores with high levels of consistency. The IBI assessment of sites sampled at different times showed high levels of temporal concordance. The IBI scores differed significantly among the geological areas, the sampling method used, and the year of survey. Overall, the results presented demonstrate the potential for New Zealand freshwater fish to be used to assess river condition at large spatial scales in New Zealand in the absence of specifically selected reference sites. This application demonstrates the effectiveness of the IBI approach even with a fauna of limited diversity and limited ecological specialisation as in the New Zealand fish fauna.