An exponential growth in groundwater extraction will greatly concern the Varuna River basin of Central Ganga alluvium. This complex issue requires proper systematic evaluations to advocate various opportunities for management strategies for groundwater sustainability. The present study aims to convey scientific assessments of the groundwater using different soft-computing techniques to determine its hydrogeochemistry and quality for averting future risk and envisaging suitable management policies. SOM (Self-Organizing Map) model involves characterizing the spatial clusters of regional hydrogeochemistry and reported a gradual increase in salinity from the northwestern to the southeastern part of the area. PCA (Principal Component Analysis) provides evidence of rock-water interactions and anthropogenic activities as responsible factors in determining hydrogeochemistry. Quality assurance is judged by various systematic chemometric indices. CCMEWQI (Canadian Council of Ministers of the Environment Water Quality Index) and IWQI (Irrigation Water Quality Index) reveal that the groundwater is suitable for drinking/domestic and irrigation use. Continuous fluxes of freshwater nourish Gangetic alluvium and generally provide excellent quality. In contrast, the analysis results notice the degradation of drinking quality from the excellent to good category (CCMEWQI) and moderate to low restriction (IWQI) for irrigation suitability. Further study of potential health risks represents the presence of carcinogenic and non-carcinogenic risks for the exposure of NO3−, F−, Pb, and Cr elements. However, the heavy metal pollution and ecological risks are low. Based on the study's findings, the estimates will support initiatives and activities at the local, regional, and national levels, as nations like India need basin-level studies. It is also recommended to consider depth-wise geochemical and temporal chemical variation for further improved studies towards risk assessment.