The Gotvand dam was built on the most important Iranian river to support a number of populated cities with freshwater, provide irrigation water for million hectares of fertile farmlands, and meet water demand for the country’s hub industrial zones. This dam is known as one of the worst engineering failures in Iran’s history because its impoundment submerged the enormous salty unit of Gachsaran evaporite formation (GEF) outcropped in the reservoir, leading to reservoir water salinization in deep layers up to several times greater than that of in the high-seas. Given the failed practical application of direct intervention strategies to control the salinity crisis, we suggested a low-cost salinity management strategy based on the reservoir operation to mitigate the dam outlet salinity and preserve the downstream environment from the salinity hazards. The three-dimensional MIKE3 model, was run to calculate the GEF dissolution rate, accumulated salt in the reservoir, and the dam outlet salinity. Then, we ran the model considering different outlet salinity levels to explore the best reservoir operation strategy to prohibit the accumulated salt in the reservoir and keep the safe salinity for downstream irrigation-use. Simulation results suggested that the GEF dissolution rate varied from 0.5 to 7 cm/hr, mainly due to incremental submergence of the GEF during multi-stage impoundment of the reservoir. Considering the final dissolution rate of 0.5 cm/hr and inlet salinity from the upstreams, salt accumulation inside the reservoir can be gradually prevented by setting the outlet salinity to its maximum historical downstream level, i.e., 1400 µmhos/cm.