The volcanic Barva and Colima multiaquifer system is crucial for the drinking water supply of about 1.7 million people, about 30% of the population in Costa Rica. The complexity of this system and the simultaneous occurrence of anthropogenic and natural processes complicate the understanding of hydrochemical and hydrogeological dynamics, both essential for groundwater protection. This research aimed to develop a model for the discrimination of groundwaters according to the main withdrawn aquifer and flow path, assess interaquifer connections, and evaluate the main hydrochemical processes governing water quality. Samples (571) from 38 sampling sites, collected quarterly from 2016 to 2020, were analyzed for nitrate, major ions, and silica. Principal component analysis and discriminant analysis exhibited and validated sample grouping according to the primary aquifer system captured, i.e., Upper Barva, Lower Barva, Upper Colima, and Lower Colima, and the occurrence of two flow paths within the Lower Barva and Upper Colima aquifers. Hydrochemical and statistical analyses showed resilience to seasonal chemical variation in deeper aquifers and also three groundwater mixing processes. Lower Barva groundwater enriches in bicarbonate, magnesium, calcium, sodium, and silica, mainly due to weathering of mafic andesitic-basaltic lavas. The Upper and Lower Colima showed higher silica and major ion content, except for calcium, indicating longer residence times, dissolution from felsic andesitic minerals, and calcium adsorption by normal ion exchange. Weathering of aluminosilicates is the primary process governing groundwater quality in the four studied aquifers, whereas cation exchange, interaquifer leakage, and anthropogenic processes might modify the groundwater chemistry.