The increasing installation of shrimp farms in vulnerable coastal areas around the world generates an environmental impact and makes it urgent to develop methodologies and studies for assessing and scaling the potential risks and sustainability of these activities. One of the main hazards of these activities is that the prolonged inundation of excavated ponds for shrimp farming allows the percolation of saltwater in the surroundings, resulting in increasing groundwater salinity. Saltwater intrusion in coastal aquifers, accompanied by salinization of soils, causes a decrease in available freshwater resources, a decline in crop productivity and the deterioration of the natural ecosystem. The coastal aquifer of Rio Grande do Norte State (Brazil) where, for years, several shrimp farm factories have been operating, reported some issues related to aquifer and soil salinization. The present study aims to assess the origin of and delineate groundwater salinization in a sector of this coastal aquifer using a low-budget procedure. The integration of hydrogeological and hydrogeochemical characterization by drilling shallow piezometers, measuring the hydrostatic level and analyzing the major ion concentrations of the groundwater has made it possible to establish that the origin of groundwater pollution in the studied area is caused by saltwater percolation from shrimp farms. The joint use of both characterization techniques has been shown to have an efficient cost–benefit ratio and less-intrusive methodology, which can be applied in other areas with similar environmental concerns.