The distribution of the benthic macrofauna of Itapocoroy Bay and the factors that influence it were analyzed within 50 sampling stations determined in a grid, covering the whole extent of the Bay. Two temporal sampling were done – one in July 2010 and the other in February 2011. Numeric describers of the community were associated with sediment characteristics, depth, salinity and temperature according to multivariate statistical analysis. A total of 4338 organisms were collected whereby 97 species were identified and classified in Polychaeta, Crustacea and Mollusca. Four faunal assemblages were found, and their spatial distribution was mainly related to depth and sediment characteristics. The first assemblage was the deepest and showed higher concentration of fine sediments, dominated by Kinbergonuphis sp.; the second assemblage - located under the mussel farm - showed high heterogeneity of sediments and was dominated by Ampelisca spp.; the third assemblage, shallower and with pebble concentration, was dominated by species of the Syllidae family; and the fourth assemblage was characterized by well sorted sediment with high percentage of sand, dominated by Prionospio sp. 1. Although the Bay is a sheltered site, the distribution of sediments showed that high energetic hydrodynamics processes operate inside it, which is able to avoid the formation of biodeposits. Nevertheless, the constant supply of organic matter and shell fragments accumulation from mussel farms are a source of stress, increasing the abundance and diversity values near the mussel farms.