RESUMO
Rodrigo de Freitas Lagoon, located in the Rio de Janeiro City, receives several types of polluted discharges. The knowledge of the sediment microfauna correlated with heavy metal and organic matter concentrations could supply important data about the conditions of the lagoon. The benthic foraminiferal assemblage presented larger diversity and more abundant samples in the lagoon entrance than in the inner area. The Ammonia tepida - Elphidium excavatum foraminiferal assemblage is characterized by dwarf, corroded and weak organisms. Agglutinated species were found only near the entrance. Low abundance values and sterility of five samples in the inner area (north/northeast) can be caused by high levels of heavy metals and organic matter. A. tepida shows negative correlation with increasing heavy metals values. PAHs and coprostanol high indexes, and the absence or low presence of microfauna in samples around the lagoon margin confirm illegal flows from gas stations and domestic sewage.