Diversity and community organization of the benthic macrofauna were investigated along the São Sebastião Channel, northern coast of São Paulo State, Brazil, and related to sedimentary variables and organic load. These important outstanding soft bottom benthic habitats are characterized by their close proximity to sources of human impact. Sampling was undertaken seasonally, using a Van Veen grab (0.1 m²) in 15 oceanographic stations, from November 1993 to August 1994. A total of 392 species were recorded and polychaetes completed nearly 50% of the fauna. Twenty three species were most numerous and frequent and comprised the baseline pool for the area. Sites were classified with respect to sediments in three site-groupings according to Arasaki et al. (2004). The finest-sediment site-group had significantly fewer species than coarser site-groups. The stations locate at the south opening and in the axis of the channel presented sediments with organic matter predominantly of marine origin, indicating the flow of open sea waters across the channel. These places showed also higher values of diversity and species richness. The site-group located along the insular side and in the channel north mouth, stood out for the significantly higher density. Although its relative small area the channel presented species richness similar to that found in the adjacent inner continental shelf. Comparisons between channel and adjacent shelf habitats are addressed in the light of ecological data.