Nitrate pollution threatens the Barva and Colima multi-aquifer system, the primary drinking water source in the Greater Metropolitan Area of Costa Rica. In addressing nitrate contamination dynamics, this study proposes an integrated approach by combining multivariate statistical analyses, hydrochemical parameters, sewage discharge, and regional land-use and land-cover patterns to assess the extent and degree of contamination, dominant biogeochemical processes, and refine the interpretation of nitrate sources previously derived solely from δ15NNO3 information. Over seven years (2015–2022), 714 groundwater samples from 43 sites were analyzed for nitrate and major ions, including two sampling campaigns for dissolved organic and inorganic carbon, nitrite, ammonium, FeTotal, MnTotal, and δ15NNO3 analyses. The findings presented elevated nitrate concentrations in urban and agricultural/urban areas, surpassing the Maximum Concentration Levels on several occasions, and oxidizing conditions favoring mineralization and nitrification processes in unconfined Barva and locally confined Upper Colima/Lower Colima aquifers. Similar nitrate contents and spatial patterns in agricultural and urban zones in the shallow Barva aquifer suggest comparable contributions from nitrogen fertilizers and urban wastewaters despite the gradual increase in urban land cover and the reduction of agricultural areas. Isotopic analyses and dissolved organic carbon (DOC) indicate a shift in nitrate sources from agricultural to urban areas in both Barva and Colima aquifers. Principal Component and Hierarchical Cluster Analyses link land use, nitrate sources, and water quality. Three distinct sample clusters aligned with forest/grassland, agricultural/urban, and urban land use, emphasizing the impact of anthropogenic activities on groundwater quality, even in the deeper Colima aquifers. The study challenges nitrate isotope mixing models, enhancing accuracy in identifying pollution sources and assessing the spatial extent of contamination by incorporating DOC and other hydrochemical parameters. Similar outcomes, with and without the use of nitrate isotopes, reinforce the usefulness of the integrated approach, providing a practical and cost-effective alternative.