Soft-bottom macrobenthic invertebrates are sensitive to natural or anthropogenic changes in aquatic ecosystems. The distribution patterns of sublittoral macrobenthic species in Guanabara Bay were studied from 2005 to 2007. Samples were collected at ten stations during six surveys throughout the rainfall regime (dry, early and late rainy). Ten replicates were collected at each station by Gravity corer or skin diving. Van Dorn bottles (bottom water) and by Ekman sediment sampler (granulometry) provided material for abiotic data. Stations were grouped into sectors (Entrance, Intermediary and Inner) based on abiotic data and location. The Redundancy Analysis (RDA) and Parsimonious RDA for all years and each annual cycle showed indicator taxa with high dominance in each sector. PERMANOVA indicated a regular seasonality between the surveys for the first annual cycle (p <0.05), and an atypical pattern for the second (p> 0.05), possibly due the low rainfall observed during this period. The mosaic of soft-bottom substrates infers structural variables, and patterns of temporal distribution were basically influenced by parameters those indicating pollution and the SACW (South Atlantic Central Water) intrusion, as well as ecological attributes among species, such as: predation, competition. The Ervilia concentrica and Cypridinidae could be used as indicators for anthropic and natural impacts in the Guanabara Bay for the Entrance sector, while Cyprideis salebrosa and Cyprideis sp. for the Intermediary sector and Heleobia australis for the Inner sector.