Urmia Lake is a hyper-saline lake in northwestern Iran that has been drying up since 2005. The main objective of this study was to evaluate the water quality in aquifers that are the main source of fresh water for the eastern plains Urmia Lake, which has been drying up due to intensive land use/cover changes and climate change. We evaluated hydro-geochemical data and factors contributing to aquifer pollution and quality variation for nine aquifers in the vicinity of Urmia Lake during the dry and wet seasons from 2000–2020. Our methodology was based on the analysis of 10 years of data from 356 deep and semi-deep wells using GIS spatial analysis, multivariate statistical analysis, and agglomerative hierarchical clustering. We developed a Water Quality Index (WQI) for spatiotemporal assessment of the status of the aquifers. In doing so, we highlighted the value of combining Principal Component Analysis (PCA), WQI, and GIS to determine the hydro-geochemical attributes of the aquifers. We found that the groundwater in central parts of the study area was unsuitable for potable supplies. Anthropogenic sources of contamination, such as chemical fertilizers, industrial waste, and untreated sewage water, might be the key factors causing excessive concentrations of contaminants affecting the water quality. The PCA results showed that over 80% of the total variance could be attributed to two principal factors for most aquifers and three principal factors for two of the aquifers. We employed GIS-based spatial analysis to map groundwater quality in the study area. Based on the WQI values, approximately 48% of groundwater samples were identified as poor to unsuitable for drinking purposes. Results of this study provide a better hydro-geochemical understanding of the multiple aquifers that require preventive action against groundwater damage. We conclude that the combined approach of using a multivariate statistical technique and spatial analysis is effective for determining the factors controlling groundwater quality.