Changes in fauna and abiotic factors in estuaries are a consequence of their exploitation; thus, bivalve mollusks, as they filter, are widely used as environmental bioindicators. The aim of this study was to analyze the existence of seasonal variation in the concentration of total coliforms (TC) and thermotolerant coliforms (Ct), in addition to correlating the data obtained with the salinity and temperature in collection areas of Mytella falcata and the soft tissue cultivated in the Estuarine Complex of Cananéia. Two biweekly samples of water and tissue were taken, for 12 consecutive months, in nine cultivation areas of M. falcata. The analysis of the water samples showed that the Fisheries Institute, Mosquiteiro, and Itapitangui have high TC densities, with respective annual averages of 772.22, 592.67, and 563.75 most probable number (MPN).100 ml−1. The highest concentrations of TC and Ct occurred in the summer, in most areas. There was a decrease in both TC and Ct with increasing salinity. However, there was an increase in Ct with increasing temperature. The soft tissue showed TC densities from 9 to 26 MPN.100 ml−1 and Ct densities from 6 to 14 MPN.100 ml−1, displaying the highest counts in the summer. Places where coliforms were found in high concentrations could indicate contamination, because Ct do not support higher salinities for a long time. Practitioner Points The general mean was 77.64 (total coliforms) and 39.35 (thermotolerant) MPN.100 ml−1. Annual average (thermotolerant) exceeded the permitted Brazilian limit in five points. Higher concentrations of total and thermotolerant coliforms occurred in the summer. In mollusk's tissue, concentrations of thermotolerant were 6.30 to 26.16 MPN.100 g−1. Coliforms' MPN varied with increasing salinity and temperature.