The gain in net power produced by Salinity Gradient plants in river mouths due to the optimal location of water intakes is analysed in this paper. More precisely, this work focuses on stratified river mouths and the membrane-based technology of Pressure-Retarded Osmosis. A methodology for this analysis is proposed and then applied to a case study in Colombia. Temperature, salinity and water discharge data were gathered at the Magdalena river mouth to develop a hydrodynamic model that represents the salinity profile along the river channel. The net power production of a pressure-retarded osmosis plant is then estimated based on the power produced at membrane level, considering different locations for the saltwater and freshwater intakes. The most adequate locations for the intakes are then deduced by balancing higher power production (due to higher salinity differences between the water intakes) with lower pumping costs (due to shorter pumping distances from the intakes). For the case study analysed, a gain of 14% can be achieved by carefully selecting the water intakes.