Identifying and quantifying water nitrate pollution is crucial for managing aquatic environment of a bay. Dongshan Bay, a significant semi-enclosed bay in the southeastern coastal area of Fujian Province, features mangrove and coral reef ecosystems at its estuary and bay mouth, respectively. Dongshan Bay is impacted by human activities such as mariculture. We quantified and analyzed nitrate pollution status in the surface waters of Dongshan Bay by measuring physicochemical parameters, stable isotopes (δ 15 N-NO 3 - , δ 18 O-NO 3 - and δ 15 N-NH 4 + ) of the surface waters, and using statistical methods including the MixSIAR isotope mixing model. The results showed that the concentrations of chlorophyll a and dissolved inorganic nitrogen in the surface waters exhibited a noticeable gradient change, decreasing from the estuary of the Zhangjiang River to the mouth of Dongshan Bay. The maximum concentrations of chlorophyll a, NH 4 + , NO 3 - and NO 2 - were 45.2 μg·L -1 , 52.67 μmol·L -1 , 379.2 μmol·L -1 and 3.93 μmol·L -1 , respectively. The nitrogen and oxygen isotope values of NH 4 + and NO 3 - in the surface waters showed significant spatial variations. According to the MixSIAR model results, nitrogen sources in the surface waters of Dongshan Bay were mainly freshwater inputs of the Zhangjiang River estuary, aquaculture wastewater, and groundwater. The freshwater input from the Zhangjiang River estuary contributed the most (25.2%), while aquaculture wastewater, groundwater and urban sewage accounted for 24.6%, 19.0%, and 15.1%, respectively. It is evident that freshwater input from the Zhangjiang River estuary is the primary source of nitrate in the surface waters of Dongshan Bay.