The groundwater contamination is a major environmental and public health issue worldwide, particularly in regions where these resources represent the primary source of drinking water for rural populations. This study aimed to assess the impact of anthropogenic activities on groundwater quality in rural areas of the Meknes region, Morocco. The primary objective was to gain a deeper understanding of these water resources in order to promote sustainable management over the long term. We interpreted the analytical data using advanced hydrochemical and statistical techniques. The findings indicate that the well water is heavily contaminated, with pathogenic bacteria and elevated levels of certain physicochemical parameters. Results reveal that the pollution is mainly due to intensive agriculture, increasing urbanization, and domestic and industrial waste. Therefore, the deterioration of water quality poses a potential threat to public health and highlights the need to adopt sustainable management practices. Such practice should include aquifer protection, elimination of contamination sources, and establishing a continuous groundwater quality monitoring network.