The determination of temporal and spatial salinity in tidal rivers is significant in supplying water for agriculture purposes, particularly where there is no controller dam at the downstream. In this research, the COHERENS model was applied to study the hydraulics of water flow, salinity distribution and transmission at the Bahmanshir river. COHERENS is a 3D multi-purpose hydrodynamic model which is coupled to biological, resuspension and contaminant models. The model was calibrated and validated against water level and two wet and dry duration periods in 2002 and 2003, as well as salinity observation during a spring tide in 2003. Three sensitivity scenarios were conducted based on different river flows and wind conditions. The model results showed that salinity intruded further upstream under scenarios with low flow and downstream wind. However, the responses of salinity stratification to different environmental forcing function were not different in various portions of the river. Finally, using time series of salinity frontal movement, spatial and temporal patterns of salinity intrusion, and the best spatial and temporal thresholds for water withdrawal along the river were assessed. The results also indicated that adopting optimal compound conditions of discharge and intermittent water harvesting could be considered as an effective and practical way to achieve qualified water for agricultural activities.