A 280-ton plant for the mass cultivation of Tetraselmis striata was operated from 2012 to 2019 to produce biodiesel fuel in western Korean coastal waters (Incheon) as a pilot project. This was the first instance globally where a microalgal mass cultivation plant for biodiesel production was implemented in coastal waters, and no prior studies had investigated the impact of microalgal mass cultivation plant on surrounding microecosystems. In this study, bioreactors (1× and 10×) mimicking a large-scale T. striata cultivation plant were installed in semi-permeable a mesocosms (5 tons) to assess their impact on the microbial ecosystem. The results showed that the release of large amounts of dissolve organic carbon (DOC) from the T. striata bioreactors. The 10× pond had a DOC concentration of 21.3 mg/L compared to the control pond of 2.1 mg/L. For the Water Quality Index (WQI), the 1× and 10× bioreactor installed mesocosms improved from Class II (Good) at the beginning of the experiment to Class I (Excellent) via decreasing nutrient levels and increasing of DO levels. However, from a biodiversity perspective, the microbial ecosystem deteriorated, with reductions in the diversity of zooplankton, ciliates, and phytoplankton. The correlation analysis and random forest variable importance measures indicated that the primary factor driving these changes was the alteration of the bacterial community due to elevated DOC levels. These findings indicate that while the mass cultivation of T. striata may improve physicochemical water quality, it has adverse effects on biological environments. Therefore, it is crucial to monitor physical, chemical, and biological factors comprehensively when cultivating microalgae on a large scale in marine environments.