Mangueira Bay is located in southern Brazil (between 30° and 32° south latitude). It is a significant regional resource that lends itself to activities such as tourism, fishing, and fish and shellfish breeding. Studies performed by Rio Grande University (FURG) have demonstrated that, due to its natural conditions, Mangueira Bay is an area of shelter and feeding for the local biota. As a result, the possibility of implementing intensive shrimp breeding has been analyzed. It is therefore important to study the hydrodynamics, water quality and sediments of this water body. This paper describes the spatial and temporal distribution of heavy metals in sediments during monitoring campaigns carried out in October 2002 and June 2003 as a part of the “Estuaries and Coastal Areas. Basis and Tools for a More Sustainable Development” (ECOSUD) project. The distribution of metals in the bed was estimated as well as the potential for resuspension due to the waves caused by typical storm conditions similar to those measured in the May 2003 campaign. This sediment resuspension in the seabed can repollute the water column. Classic expressions were used to estimate the wind-induced water waves, the resuspension rate and the concentration of suspended material. The results show differences in spatial distribution between the two campaigns, but in both cases the south of Mangueira Bay was found to be the proper area for aquaculture. Furthermore, in all of the sediment samples analyzed, the different metals were present in concentrations under the limits stipulated by the Canadian Environmental Quality Guidelines of the Canadian Environmental Protection Agency (CEPA). The calculation of sediment resuspension demonstrated that conditions favor shrimp breeding along the southwest coast under typical winds from the west, especially in the southern part of Mangueira Bay.