The total phosphorus (TP) concentration, as the primary limiting eutrophication factor in the Mahabad Dam reservoir in Iran, was studied, considering the combined impacts of climate change, as well as the scenarios on changes in upstream TP loadings and downstream dam water allocations. Downscaled daily projected climate data were obtained from the Beijing Normal University Earth System Model (BNU-ESM) under moderate (RCP4.5) and extreme (RCP8.5) scenarios. These data were used as inputs of a calibrated Soil and Water Assessment Tool (SWAT) model of the watershed in order to determine the effects of climate change on runoff yields in the watershed from 2020 to 2050. The SWAT model was calibrated/validated using the SUFI-2 algorithm in the SWAT Calibration Uncertainties Program (SWAT-CUP). Moreover, to model TP concentration in the reservoir and to investigate the effects of upstream/downstream scenarios, along with forecasted climate-induced changes in streamflow and evaporation rates, the System Dynamics (SD) model was implemented. The scenarios covered a combination of changes in population, agricultural and livestock farming activities, industrialization, water conservation, and pollution control. Relative to the year 2011 in which the water quality data were available, the SD results showed the highest TP concentrations in the reservoir under scenarios in which the inflow to the reservoir had decreased, while the upstream TP loadings and downstream dam water allocations had increased (+29.9%). On the other hand, the lowest TP concentration was observed under scenarios in which upstream TP loadings and dam water allocations had decreased (−18.5%).