The severe water quality pollution of the Bohai Sea impacts both the ecosystem and the economy of the region. This study assesses the water quality of the Bohai Sea using a two-year (2020–2021) dataset to investigate the spatial distribution and sources of contamination. Multivariate statistical analysis methods, including principal component analysis (PCA), cluster analysis (CA), and discriminant analysis, are employed. Thirteen chemical indicators are analyzed through PCA, resulting in the extraction of three principal components that reflect different pollution sources related to domestic, industrial, and agricultural activities. Additionally, the corresponding water quality index (WQI) is calculated to categorize the water quality into three levels using CA. The PCA-based WQI method is feasible and shows similarities to the traditional WQI method. Higher pollution levels are observed in Panjin and Tianjin, while Huludao, Yantai, and Dalian exhibit relatively good water quality. The results indicate complex, multifactorial pollution causes in the Bohai Sea, including eutrophication, heavy metal contamination, and ammonia pollution. These findings can guide region-specific water quality management: Panjin should control heavy metal discharges from industry and transportation, while Tianjin requires improvements in runoff management of ammonia-based fertilizers. Together, these strategies support the ecological and sustainable development of the Bohai Sea.