Urbanization impacts, especially stormwater runoff and pollutant discharge, pose ecological threats to coastal ecosystems globally. Long-term environmental monitoring datasets and assessments are used to quantify anthropogenic impacts on ecosystem health. This study synthesized twenty years (2002–2021) of water quality data from the National Estuarine Research Reserve System-wide Monitoring Program at the understudied Masonboro Island Reserve (North Carolina, United States) and provided an analytical methodology that can be applied to other Reserves and monitoring programs world-wide. Time series and correlation analyses of biological, chemical, and physical water quality parameters were used to identify spatiotemporal trends of nutrient dynamics and phytoplankton biomass at three stations within a 5-km stretch of the Atlantic Intracoastal Waterway. Heterogenous water quality conditions were observed between stations, especially for chlorophyll a, and were influenced by the relative proximity to marine waters, human developments, and urban tidal creeks. Long-term trends indicated significant water quality changes (i.e., increased chlorophyll a, reduced pH and salinity) related to anthropogenic influences. An unexpected and rapid shift in nutrient dynamics occurred around 2007, marked by significantly decreased ammonium and orthophosphate concentrations, which considerably reduced DIN/DIP ratios. This positive change was potentially influenced by sewage infrastructure improvements and stormwater wetland construction, removing waste-derived nutrients that previously entered the ecosystem. Impacts of major storms were also observed with weeks of hypoxia and low salinity following Hurricane Florence. These findings emphasized the value of long-term trend analyses of monitoring program data at multiple sites and provided insights into the significant water quality impacts of urbanization and benefits from wetland protection. This study further encourages the evaluation of long-term water quality monitoring datasets in estuarine environments globally.