Groundwater quality plays a crucial role in providing drinking water and ensuring the health of rural communities, and its variations can affect public health and the sustainability of water resources. In this study, the quality of rural wells in Mahmoudabad County was assessed over the period 2020–2025 using the WQI and NSFWQI indices, along with statistical methods including Pearson correlation analysis and k-means clustering. The results indicated that over 80% of the water sources fall within the “good” to “excellent” categories; however, increased concentrations of nitrate, total hardness, and TDS in some wells highlight the impact of agricultural activities and the region’s hydrogeological conditions. Correlation analysis revealed strong relationships between chemical parameters and quality indices, while clustering divided the water sources into three distinct quality groups, facilitating prioritization for monitoring and resource management. Spatial distribution of water quality also showed differences related to well depth, formation type, and surrounding land use. These findings emphasize that periodic monitoring and pollutant management are essential to maintain water quality and reduce contamination risks.