Phytoplankton is essential in coastal marine ecosystems, aiding ecosystem stability and development of marine economy. Coastal ecosystems, as a transitional zone, feature complex, variable environmental factors that significantly affect phytoplankton growth. To assess the factors influencing the growth of phytoplankton in the bay area, this study measured chlorophyll a (Chla), nutrients, and four antibiotics (sulfamethoxazole, sulfadiazine, ciprofloxacin, and enrofloxacin) in seawater, as well as total nitrogen and total phosphorus contents in sediments at 25 stations in Lianzhou Bay. Principal component analysis and the risk quotient (RQ) were utilized for analysis and assessment. The results indicate that the factors influencing Chla concentrations are inconsistent between the nearshore and offshore areas of Lianzhou Bay. Specifically, abundant nutrients, high ammonia levels, and low enrofloxacin concentrations are the primary factors contributing to high Chla concentrations in the nearshore area. In contrast, hydrodynamic conditions, feeding by cultured shellfish, and adequate lighting collectively shape the distribution characteristics of Chla in the offshore area. Additionally, the ecological risk posed by antibiotics in this bay is relatively low. The findings of this study provide scientific evidence for local management of marine pollution sources and the optimization of aquaculture models, which is of great significance for sustainable utilization of marine ecological resources.