The Mondego estuary consists of two arms, north and south. The north arm is deeper, while the south arm is largely silted up, causing freshwater to flow primarily by the north arm. Environmental stress is severe. essentially due to harbour activities, salt-works, aquaculture farms. and nutrients and chemicals discharged from agricultural areas of the lower Mondego river valley. From December 1989 to September 1990 a study of the subtidal macrofaunal community was carried out. Polychaetes were found to be the most abundant macrofaunal group of the Mondego estuary subtidal community, representing about 34.5 % of the species and 63 % of the individuals sampled. Both biological and physicochemical data were analysed by principal components analysis (PCA), and data on the Polychaete fauna was also analysed with regard to spatial and temporal variations of total abundance. The Mondego estuary seems to present an impoverished subtidal Polychaete fauna with regard to the number of species, although the south arm presents enhanced populations. In the inner areas of the south arm. the Polychaete fauna is characterized by abundant populations of Amage adspersa, followed by more sparse populations of Capitella capitata, Heteromastus filiformis, Polydora ciliata, and Streblospio shrubsolii. Moreover, the number of species was roughly stable through the year, and Polychaetes exhibited by far the most elevated abundances found in the estuary. In the north arm, the Polychaete fauna was characterized by Hediste diversicolor and Streblospio shrubsolii, almost restricted to the upstream section, followed by the sporadic occurrence of other species. The north arm exhibited an extremely impoverished Polychaete fauna, both in number of species and total abundance. as compared to the south arm. In the downstream area of the south arm and near the mouth of the estuary the Polychaete fauna was characterized by the occurrence of a mixture of uncommon species e.g. Eulalia sp., Eteone picta, Glycera convoluta, Lagis koreni, Nephthys spp.,