Groundwater quality assessment is crucial for sustainable water resource management in Maharashtra, India, where groundwater helps for main water sources for irrigation, domestic, and industrial sectors. Despite numerous studies on regional groundwater quality, there remains a lack of integrated research combining hydrogeochemical analyses with advanced spatial and statistical techniques. This study addresses this gap by developing a comprehensive groundwater quality assessment framework that uniquely integrates hydrogeochemical analyses, geographic information system (GIS) techniques, water quality index (WQI), and multivariate statistical approaches in the Morna River Basin. A total of 82 water samples were analyzed for physicochemical parameters in the pre-monsoon (PRMS) and post-monsoon (POMS) seasons. The WQI analysis revealed that 46.15% of samples exhibited excellent water quality, while 48.72% showed good quality during both seasons, though a notable quality decrease was observed during the POMS. Correlation analysis identified significant positive associations (p < 0.05) between key parameters, including Mg-TH, EC-pH, and Ca2+-TH. Principal component analysis identified six components explaining 75.534% of total variance in PRMS, with the first component contributing 17.437%. In POMS, five components explained 70.963% of variance, with the first component contributing 20.653%. Factor analysis revealed that mineral dissolution, agricultural activities, and anthropogenic inputs were the primary factors influencing the water chemistry. The spatial distribution maps generated through GIS analysis identified hotspots of contamination. This integrated approach provided a robust framework for understanding the complex interactions between natural and anthropogenic factors impact on the groundwater quality. The results suggest regural monitoring of water quality and an identified hotspots and implementation of rules and regulations on the agricultural practices and waste disposal. This research contributes to support of groundwater management strategies and provides a methodological framework appropriate to similar hydrogeological settings in other area or worldwide.