<p>Mangroves are crucial for safeguarding coastal regions and estuary ecosystems. Ecosystem services provided by the mangroves are affected by the water quality, so it is crucial to assess the water quality comprehensively. Historically, lack of comprehensive assessment has been a significant deterrent to the precise assessment of mangrove water quality. This research thoroughly evaluates Mangrove Water Quality (MWQ) in the Hung Yen Mangrove (HYM) located in Northern Vietnam, which extends about 50&#xa0;km from the shoreline. Water quality was assessed at 47 sites inside the HYM during the rainy and dry seasons of 2022 using a multi-index approach. Five indices, Comprehensive Pollution Index (CPI), Organic Pollution Index (OPI), Water Quality Index (WQI), Contamination Index (CI), and Trace Metal Pollution Index (TPI), were applied to capture diverse dimensions of water quality. Of indices used for MWQ assessment, the CPI classification was Moderately Polluted and Heavily Polluted, whereas, as per OPI falls in Polluted and Heavily Polluted; WQI as Extremely polluted and Medium level; CI as Low to Medium pollution levels; and TPI indicates certain locations have pollution concerns during the dry season. The results indicate that CPI is the most reliable index for MWQ assessment, and TPI is essential for evaluating trace metal pollution. Principal Component Analysis (PCA) indicates aquaculture as a major pollution source. Further, the study highlights the integral role of the HYM ecosystem in supporting natural water purification processes through the bio-filtration mechanism. It provides valuable insights for policymakers to mitigate and prioritise mangrove health in the conservation of global coastal ecosystems through the case study of HYM.</p> Graphical Abstract <p></p>