The article discusses the original equivalent level method developed for assessing the water quality of the Rybinsk Reservoir, and its application to forecasting the negative environmental impacts that are highly likely to occur if the projects to restore the land lost to impoundment are implemented. It is shown that the dependencies of the concentrations of certain inorganic ions and petroleum products in the reservoir on its water level are closely modeled by the decreasing exponential regression. For 12 hydrochemical indicators, the regression coefficients were graphically determined, and their statistical significance was verified by the Fisher’s and Student’s tests. The resultant relationships were used to calculate the maximum equivalent levels, below which the environmental impacts can be compared with exceeding the maximum allowable concentrations (MAC). It is shown that an important role in the study of the dynamics of the reservoir’s hydrochemical parameters belongs to the rate of change in the concentration of chemicals due to changes in the water level. The rates of increase in the concentration of 12 hydrochemical indicators upon crossing the Rybinsk Reservoir’s normal retention level (101.81 m BHS) were estimated. The highest rate is demonstrated by Mn2+ cations (the only indicator for which the rate exceeds 1 MAC/m). Considering the changes in the Rybinsk Reservoir water quality predicted by using the proposed methodology, there is reason to believe that the implementation of projects for partial drainage of the flooded land by lowering the reservoir’s normal retention level to 98 m BHS will cause 9 out of 12 substances to rise above the MACs for fishery reservoirs, while during 2018–2024, only 4 indicators exceeded their MACs. Thus, implementing such projects is unadvisable. We have particularly studied the processes of Mn2+ and Fetot influx into the reservoir, since other authors have reported these elements to have exceeded the permissible levels in other reservoirs, but this was often associated with the region-specific geochemistry. A scenario is considered in which the reservoir’s level will be fixed at a constant elevation over a long period of time. The supposition is that the water quality in this case will be consistently affected.