With the growing socioeconomic activity of mussel farming on Santa Catarina’s coast, the identification of new cultivation sites became necessary. Among a variety of methods used for the analysis of potential producing areas, studying of the mussel physiological rates may be considered as one of the most appropriated, specially when addressing the monitoring of sites already established and the negative effects of environmental pollution. This report presents a preliminary comparison between two areas of cultivation in the northern coast of the state (municipalities of Penha and Bombinhas). In both locations, environmental data (temperature, salinity and seston) and physiological parameters of the mussels (growth, and filtration, respiration and assimilation rates) were analysed. Our findings suggested a direct relationship between temperature and mussel growth rate and also between salinity and respiration rates for both areas. The seston concentration showed a high environmental variability as a response to the continental drainage. In addition, the filtration and assimilation rates seemed to be influenced by the stages of embryonic follicle maturation. In terms of production, the sites showed larger differences during the colder months as compared to the warmer ones, when the results were quite similar. More conclusive results are dependent of studies conducted along a complete annual cycle.