The effects of the 3 main wastewater discharges on the benthic fauna of the Manawatu River were studied between March 1979 and January 1980. At least 4 replicate Surber samples were taken from each of 6 sites, on 5 occasions during this period.Deleatidiumsp. (Ephemeroptera),Hydorasp. (Coleoptera), and the Chironomidae were the most useful indicator organisms, according to a ranking system based on the occurrence of significant differences (P<0.05) between populations at different sites. These taxa exhibited significant differences between sites in about 70% of all inter‐site comparisons, using Mann‐Whitney U‐tests. The Coefficient of Similarity was successful at summarising the comparisons between the clean‐water and down‐stream sites, ranging between 95% similarity to the clean‐water site for a recovery site in winter, and less than 10% similarity to the clean water site for the lower reaches in summer. It is suggested that relative indices may be more appropriate than absolute indices for measuring water pollution. Water quality, indicated by species diversity, was generally good (allowing for the effects of agricultural runoff), although midsummer organic loading induced marked changes in benthic species composition, including the disappearance ofDeleatidiumsp. from several sites.