Stream salinity management is of prime importance for ensuring environmental sustainability of rivers, streams, lakes and other water bodies. Saline groundwater inflows are the main cause of deteriorating quality of stream flows; especially during periods of low flows. The Murray-Darling Basin is a good example for reducing groundwater recharge from irrigated agricultural areas with successful implementation of land and water management plans (LWMPs). In most cases, these plans help minimize the influence of saline groundwater flows on the stream salinity, as a preventive measure. As a remedial measure, this paper introduces a simple but an innovative approach for regulating saline groundwater inflows to natural streams in irrigated agricultural areas. The approach uses the flap gate with an automatic lowering and raising mechanism. During low stream flow, this gate is kept in a raised position. Depending upon the upstream inflows, the ponding situation will develop hydraulic gradient away from the stream; groundwater inflows to the creek will become minimal. During high stream flows, the gate is kept in a lower position to let the diluted water flows through the stream uninterrupted. To install, operate and manage such gates on multiple sites along the stream(s), the individual control panels can be joined into a central control station via telemetric link up. This approach, which holds a key for successfully regulating groundwater induced salinity to natural streams, should be considered in conjunction with other LWMPs to improve stream salinity in an irrigated agricultural area.