The Shapour River, with a catchment area of 4254 km2, is a major river system in southern Iran. While the upstream river flow (the upper Shapour River) is fresh, it becomes extremely salinized at the downstream confluence of the Shekastian saline tributary and the entering nearby Boushigan saline spring. Then, the river passes via the Khesht plain and finally discharges into Raeisali-Delvari storage dam which went into operation in 2009. Over the 2006–2019 period, reduced precipitation and over-utilization of freshwater resources resulted in ~ 72% streamflow reduction in the Shapour River. Due to not using the saline waters for irrigation, drinking, and industrial purposes, the ratio of saline-outflow of Shekastian tributary and Boushigan spring to fresh-outflow of upper Shapour River increased by ~ 3 times; consequently, river salinity fluctuation domain at the Khesht plain inlet dramatically increased from 2.1–4.0 dS m−1 to 3.7–26.0 dS m−1. It resulted in major economic damages to the agricultural sector of middle Shapour River. On the seasonal timescale, consecutive processes of salt accumulation during irrigation season of the Khesht plain date orchards and then salt drainage during the rainy season have adjusted salinity fluctuation domain from 3.7–26.0 dS m−1 at the plain inlet to 5.2–8.9 dS m−1 at the plain outlet. In the lower Shapour River, storage/mixing of fresh/saline inflow waters in the Raeisali-Delvari reservoir has adjusted strong river salinity fluctuation domain from 0.9–10.7 dS m−1 at the reservoir inlet to 3.6–5.5 dS m−1 at the reservoir outlet. The success of the Raeisali-Delvari reservoir for salinity adjustment is due to its suitable location on the Shapour River, by being situated downstream of all main river tributaries with natural saline/fresh sources of water.