This study assessed the levels of water qualities and microbials contamination of inland olive flounder farms in Jeju in the summers from 2015 to 2017. Three farms (A-C) located in a concentrated area using mixing coastal seawater and underground seawater and one farm (D) located in an independent area using only coastal seawater were selected. Total ammonia nitrogen (TAN) reached a maximum of 0.898 ± 1.024 mg/L as N in the coastal seawater of A-C, which was close to the limit of the water quality management goal of the fish farm. TAN in the influent from A-C was up to three times higher than that of D, so that the discharged water did not spread to a wide range area along the coast and continued to affect the influent. TAN of the effluent in A-C increased by 2.7-4.6 times compared to the influent, resulting in serious self-pollution in the flounder farm. Heterotrophic marine bacteria in the influent of A-C was about 600 times higher than D, and the discharge of A-C was increased by about 30 times compared to the influent.