Critical to global water security, aquifers represent a strategic resource that must be rationally exploited to ensure their future availability and to guarantee the socioeconomic and environmental development of a region. This paper assesses the chemistry of groundwater and evaluates its quality status using a hybrid framework that includes the use of a regionalized Groundwater Quality Index (GQIR) in conjunction with a GIS-based geostatistical tool. The proposed hybrid approach is presented through a case study conducted in a peri-urban microbasin in Northeast Brazil with an unconfined aquifer system as the main source for public water supply. For this purpose, a total of eight wells were sampled during the rainy and dry seasons throughout 2019. Twelve hydrogeochemical parameters were evaluated, of which only phosphorus exceeded the maximum allowable limit in 75% of the cases. The geostatistical distribution maps made it possible to identify the aquifer areas most affected by domestic effluents, agriculture and livestock farming. The water quality parameters are mainly affected in wells located in highly urbanized and agricultural areas (P1–P5). Despite this, the GQIR ranged from 61.40 to 75.59 (rainy season) and from 55.04 to 72.92 (dry season). Although there was a relative worsening of the water quality in the dry season, in both cases, the water quality can be classified as Good (51 < GQIR ≤ 79). This hybrid approach allows water resource managers to prioritize areas in which mitigation and aquifer monitoring actions are most needed.