This study assesses an estimate of the potential rainfall infiltration in the northern area of Loreto in the state of Baja California Sur, Mexico. The basins of Gombedor, Loreto, and San Bruno are included. The analysis is based on precipitation and temperature data from the climatic stations near the municipality of Loreto. This study is in response to the scarcity within the matter and the urgency that the pressure on water resources represents to the region. Precipitation and temperature models were estimated using the Kriging interpolation method. The evapotranspiration, runoff, and potential infiltration were calculated from these models. The results obtained were 5.37 Mm3 year-1 for the Gombedor basin, 13.37 Mm3 year-1 in the San Bruno basin, and 7.62 Mm3 year-1 north of Loreto. The San Bruno basin is where the extraction wells that supply the city of Loreto are located. In the San Bruno basin, a potential recharge of 1.97 Mm3 year-1 was estimated with an average annual rainfall of 207 mm. Rainfall infiltration is one of the most important sources of aquifer recharge, in addition to groundwater flows and induced recharge. The hydrogeological model allows for addressing the situation of the basin to develop management strategies. These models can be efficient in regions without surface waters and readily available information. Moreover, hydrogeological models provide a good forecast for the Loreto region since the data are insufficient. The results for the variables show the potential of the methods based on techniques of Geographical Information Systems and geostatistics.