Contaminants derived from urban runoff have been shown to accumulate in estuarine sediments, reaching concentrations potentially capable of causing biological effects. Demonstration of effects, however, is difficult due to strong natural environmental gradients and the effects of past or present point-sources of contamination. We used multivariate methods to test two hypotheses relating to the effects of urban-derived contaminants on estuarine benthic communities. First, that patterns of distribution and abundance of benthic invertebrates in two urbanised estuaries would be different from those in two non-urbanised estuaries. Second, that the distributions of benthic invertebrates within and among the four estuaries would be related to those of urban-derived contaminants. Concentrations of contaminants were larger in estuaries with urbanised catchments and concentrations of Cu, Pb, Zn and DDT in some samples exceeded those at which biological effects may be expected to appear. Tests of differences in composition of benthic communities among estuaries showed that the two urban estuaries were not significantly different, but that they differed from both rural estuaries, which also differed from each other. Distributions of benthic invertebrates were significantly related to those of environmental variables, and were ordinated along axes that correlated with both natural environmental variables (nature of the sediment, position in estuary) and contaminants. Differences in faunas between the urban and non-urban estuaries were not, however, clear-cut and nor were relationships between faunal assemblages and environmental variables (including contaminants) consistent between two times of sampling.