Detecting and understanding long-term and evolving changes in water quantity and quality is critical for sustaining ecosystem function and guiding adaptive watershed management under changing socio-economic conditions. In this study, we assess both monotonic and evolving (non-stationary) trends in streamflow and water quality across the Mobile Bay Watershed (MBW) in the Northern Gulf of Mexico. We combine traditional Mann-Kendall (MK) and Sen’s slope estimators with a Rolling Window Mann-Kendall (RW-MK) framework to capture persistent and episodic changes in hydrological and biogeochemical dynamics. Using observed streamflow and water quality records from 1982 to 2020, we examined trends in annual, monthly, and ecologically relevant flow metrics, alongside trends in nutrients and sediment concentrations, water temperature, dissolved oxygen, and salinity levels. Whole-period MK analysis revealed widespread streamflow declines (59 of 61 sites) and significant increases in nitrate (19 of 29), organic nitrogen (12 of 19), organic carbon (10 of 15), and water temperature (24 of 31), while phosphate, ammonium, and sediment concentrations generally decreased. These changes coincided with urban expansion, reductions in agriculture and forest cover, and regional climate shifts marked by increasing temperature (~0.3 °C decade) and precipitation (+33 mm decade). The RW-MK analysis revealed additional “trends within trends,” identifying sub-periods of significant declines in both low and high flows and temporal shifts in estuarine salinity closely correlated with freshwater discharge variability. By integrating monotonic and rolling-window analyses, our findings indicate that hydrological and biogeochemical trends in the MBW are not temporally uniform but evolve in response to interacting climate and land-use drivers.