Coastal waters may appear compliant with regulatory standards while already experiencing nutrient stress. In Mundu, northern Java, we assessed ecosystem health by combining correlation analysis with multiple water quality indices (WQIs). Surface water from nine stations was analyzed for temperature, salinity, dissolved oxygen, NO2, NO3, PO4, and NH3 during the rainy season. Results showed pronounced spatial gradients with elevated nutrient levels (NO3 > 0.15 mg/L, PO4 to 0.04 mg/L) near estuaries and urban areas, exceeding national thresholds. Correlation analysis revealed strong linkages among variables, including ammonia total rising with temperature (r = 0.878), reflecting warming-enhanced mineralization, and a salinity–oxygen paradox where higher salinity waters maintained elevated oxygen (r = 0.712). WQI outcomes diverged: STORET (–21) and PI (6.28) classified the waters as moderately polluted, whereas BCWQI (2.26) and CWQI (97.89) showed excellent quality. These inconsistencies highlight the limitations of relying on a single index and point to the need for integrated frameworks that link compliance-based thresholds with ecological signals. It provides valuable insights into the health and productivity of aquatic environments for monitoring data-poor tropical regions. The findings provide early warning of eutrophication risks and strengthen the scientific basis for evaluating the Clean Waters sub-index of Indonesia’s Ocean Health Index (OHI) status
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