Dockyards and harbors are recognized as being important locations where sediment-associated pollutants can accumulate, which constitutes an environmental risk to aquatic life due to potential uptake and accumulation of heavy metals in the biota. The aim of this paper is to assess the concentrations and the effects of some heavy metals in the benthic foraminifera assemblage in Niterói Harbor. Low concentrations in the benthic foraminifera as well as the dominance of indicative species such as Ammonia tepida, Buliminella elegantissima and Bolivina lowmani can be associated with an environment under stress. In addition, the occurrence of test abnormalities among foraminifera may represent a useful biomarker for evaluating long-term environmental impacts in a coastal region.