The margins of Brazilian rivers are considered Permanent Preservation Areas—APPs, due to the riparian forest’s water resource preservation capacity. However, a significant portion of the Brazilian Atlantic Forest biome, in which the Jacaré River basin is located, has suffered increasing deforestation over the past decades. This research aimed to use a methodology integrating Geographic Information System (GIS), fuzzy logic, Analytic Hierarchy Process (AHP), and sensitivity analysis to model the selection of riparian protected area stretches that presents the best successful riparian forest reforestation using a real case, the Jacaré river basin, whose characteristics are often in Brazilian watersheds. To identify the main drivers that influence reforestation success, we carried out a broad and detailed bibliographic research. To establish the relative importance among the drivers, we conducted a survey with experts. The results showed that areas with moderate chances of reforestation prevail in the studied region. Due to the areas’ distribution pattern, a significant portion of the best sites were grouped, forming regions that create environments that favor aquatic and riverside life development and ecological balance maintenance, thus bringing together fundamental characteristics to improve water resources sustainability. The best sites have dystrophic or eutrophic soil, with a slope of up to 15%. Besides, they are mainly covered by grass and are close to forest fragments with low vulnerability.