In Santa Catarina, the production of marine molluscs, mainly Crassostrea gigas and Perna perna, has increased considerably during the last decade. In order to conduct a seawater characterization of culture sites a monitoring program has been developed in five different locations along Santa Catarina's coast (27 degrees 23 ' and 27 degrees 55' S; 48 degrees 40' and 48 degrees 20'W). From August 1998 to December 2002 data was collected on physical-chemical parameters, chlorophyll a, and suspended matter. It was not possible to notice any significant trends of temporary variation for the different factors in the same location. The major differences observed were related to comparisons among the different parameters at different times of the year in the different places of study, which reflected the local environmental and seasonal variations. In the Northern bay of Santa Catarina's island, we found a larger chlorophyll a concentration compared to the Southern bay, 3.7 and 2.7 mu g.L-1, respectively. The concentration of total suspended matter was also larger in the Northern Bay than in the Southern Bay, 21.7 and 10.7 mu g.L-1, respectively. Outside the bay chlorophyll a averaged 1.5 mu g.L-1and the total suspended matter 8.9 mu g.L-1. Data indicates a relatively larger abundance of food for the molluscs in the Northern bay; however, that food is less available because it demands larger energy efforts for its selection and metabolization. We strongly need a more rigorous follow up of the production of marine molluscs in relation to the sites used for their cultivation.