Çardak Lagoon is one of the most important marine environments in the Turkish Strait system, which is home to a variety of organisms. The lagoon is currently under stress and faces the risk of heavy pollution. For this reason, the present state of the lagoon was monitored in this study. During sampling from October 2018 to June 2019, the levels of indicator microorganisms fluctuated up to 4.04 Log10 cfu 100 ml−1 and their presence was found to be higher in warmer seasons. The highest positive correlations were observed for total coliform levels with salinity and chemical oxygen demand, whereas the highest negative correlations were found between the levels of fecal coliforms, pH and temperature.