Aquatic ecosystems face significant impacts from human-related stressors, demanding a deep understanding of their dynamics and interactions for effective management and restoration. The Albufera Lake (Valencia, Spain) presents a complex scenario of multiple interacting stressors affecting its eutrophic status. In this study, we compiled a 50-year dataset and used Generalized Additive Models (GAMs) to analyse the dynamics of the main stressors affecting the ecological status of the Albufera Lake. Then, we assessed their individual and combined effects on eutrophication using chlorophyll-a concentration as a proxy and provided recommendations to enhance water quality. Overall, we found a decrease in annual water inflow and a clear effect of rice cultivation on the seasonal patterns of the Lake's residence time. Our analysis also shows an increase of average water temperature of 2 °C for the last 50 years, and an increase in the frequency and severity of heat waves. In contrast, we found a slightly negative long-term trend in conductivity, despite the occurrence of seasonal peaks in summer. Regarding nutrients, we identified a clear reduction of total phosphorus (from 1.08 mg/L in 1987 to 0.20 mg/L in 2022), while nitrate concentrations have been rather stable. Our results also point at an increase of toxic pressure exerted by organic and inorganic contaminants during the last years, with seasonal toxicity peaks occurring during rice field drainage periods. The main stressors affecting the chlorophyll-a levels were found to be temperature, water scarcity, and nitrate concentration as well as the interactions between temperature and conductivity, conductivity and nitrate, conductivity and water scarcity, and nitrate and total phosphorus. We found that stressor interactions are highly dynamic and result in synergistic and antagonistic effects that vary according to different stressor levels. Finally, our GAM framework points to two potential scenarios: increasing freshwater inflows or deregulating hydrology to allow seawater exchange, which are key for improving the ecological status of the Albufera Lake in the short-term.