Guanabara Bay (GB) is considered to be one of the most polluted environments of the southern Brazilian coastline. This typical estuarine system is impacted by the heavy discharge of both industrial and domestic waste from the Rio de Janeiro metropolitan area. The mollusc community structure and distribution was investigated between 2000 and 2001, using a three month sampling design of 38 stations, according to austral seasons. Species abundance was aggregated into progressively higher taxa matrices (genus, family, order) and were analysed using multivariate techniques. Mollusc distribution in GB varied significantly in space and time and was probably ruled by the organic enrichment effects of hypoxia and altered redox conditions coupled with prevailing patterns of circulation. Within the sectors of GB an increasing gradient in mollusc diversity and occurrence was observed, ranging from the azoic and impoverished stations in the inner sector to a well-structured community in terms of species composition and abundance inhabiting the outer sector. The non-metric multidimensional scaling (nMDS) and cluster analysis showed similar results when species were aggregated into genera and families, while greater difference occurred at coarser taxonomic identification (order). The literature about taxonomic sufficiency has demonstrated that faunal patterns at different taxonomic levels tend to become similar with increased pollution. In Guanabara Bay, an analysis carried out solely at family level is perfectly adequate to describe the ecophysiological stress. Further aggregation to order level changed the perceived patterns of differences. However, a different taxonomic resolution can be chosen depending on the type of ecological patterns investigated.