Sediment macrobenthos of the Upper Otago Harbour, south‐eastern New Zealand, was surveyed in 1993. Replicate samples (0.1 m2sieved on 1 ‐mm mesh) were taken using a diver‐operated suction sampler from 15 stations, including some suspected to be contaminated. Multivariate analysis of abundance data was used to examine patterns of benthic community structure and their relationship to environmental variables: sediment grain size, organic content, heavy metal concentration (V, Cr, Mn, Co, Ni, Cu, Zn, Cd, Pb), sea‐floor temperature, dissolved oxygen concentration, water depth, and macro‐algal content. Samples from Sawyers Bay, an area previously identified as impacted by sewage and industrial waste, were set apart from all other stations. A combination of percent sand, macro‐algal content, water depth, and chromium concentration correlated best with the observed community structure.