Iran is not a rich freshwater country. Many dams have been constructed in Iran during the last decades. As better reservoir operation is always important, discovering different properties of water in the reservoirs can be used for developing operating policies. Shahid Rajaee dam with a large reservoir is located in Mazandaran Province, Iran. Shahid Rajaee reservoir falls in the warm monomictic stratified category. Available data from the period 2012 to 2015 have been used for modeling temperature, Dissolved Oxygen (DO) and Total Suspended Solids (TDS) in this reservoir using CE-QUAL-W2. Temperature–depth diagrams have been drawn and thermocline characteristics have been determined from the first-year data. Moreover, two operation scenarios have been defined. The effect of 20% reduction of the TDS loads in both upstream rivers or the major river on the TDS concentration of the reservoir at a specific point has been evaluated. The model's results show 20% and 14.2% reduction in the maximum values of the TDS time series, respectively and 19.4% and 13.4% reduction in the minimum values of the TDS time series, respectively. Moreover, the Iran Water Quality Index for Surface Water Resources – Conventional Parameters (IRWQISC Index) Index has been used for determining the reservoir's water quality. The index showed a ‘good’ water quality for the reservoir before and after the salinity reduction scenario.