River mouths are locations with high theoretical potential for harvesting salinity gradient energy (SGE) since waters of different salinities are abundant in these places. However, the net extractable SGE potential—or site-specific potential (SSP)—is determined not only by the available natural resources but also by the energy consumption required for operating the power plant. Particularly, the required inputs for water pretreatment prior to energy generation to preserve the proper functioning of the membranes and other components within the systems, have been identified as a major drawback for SGE generation from natural waters. In this paper, the required energy consumed during water pretreatment was estimated, comparing conventional and membrane-based methods. This energy input was included in the formulations of the SSP, as a function of the design flow of the power plant and was used to assess the extractable SGE potential at the Magdalena River mouth, a top-ten system for SGE generation worldwide. The results showed that water pretreatment produced an important reduction of the SSP in the case study, while high potentials were still found for appropriate design flows.