The Indian Punjab state is drained by the four rivers, along with a well-connected network of canals, and is now dealing with a slew of water quality issues and problems. In this study, basin-wise hydrogeochemical modelling of 323 groundwater samples and identification of NO3- and F- enrichment pathways in aquifer systems of Punjab were studied using different plots and multivariate statistics. To evaluate the groundwater quality and human health risks, an entropy-based water quality index and Monte Carlo simulation were used, respectively. Spatial distribution of NO3- indicated that its very high values were prominent in parts of southwestern Punjab falling under LSRB, along with few pockets in eastern and northeastern Punjab falling under MSRB and GRB. High NO3- values (> 45.0mg/L) were found in 15.0% of Ravi River Basin (RRB) groundwater samples, 22.86% of Beas River Basin (BRB), 23.52% of Middle Sutlej River Basin (MSRB), 36.9% of Lower Sutlej River Basin (LSRB), and 21.31% of Ghaggar River Basin (GRB). The spatial distribution of NO3- revealed elevated concentrations (> 100mg/L) in the southwestern part of Punjab, particularly in LSRB and localized pockets in the eastern and northeastern areas of Punjab within MSRB and GRB. High F- concentration (> 1.5mg/L) was observed in 15.12% and 21.31% groundwater samples of LSRB and GRB, respectively. Spatially southern parts falling under LSRB and GRB reflected high F- content (> 1.5mg/L) in groundwater. In LSRB, evaporative and anthropogenic processes influence the groundwater quality. The results of interionic relationships and statistical analysis revealed that NO3- has anthropogenic origin and that is being aggravated by leaching,the evaporation processes, animal excreta, septic tanks and irrigation return flows in LSRB and GRB, while F- is geogenic in nature. Hazard index (HI) values in 14.63%, 22.2%, 24.6%, 49.58%, and 34.42% samples for adults and 21.95%, 27.7%, 42.0%, 72.3%, and 52.46% samples for children were higher than unity in RRB, BRB, MSRB, LSRB, and GRB, respectively. The basin-wise demarcation of various groundwater quality parameter and assessment of human health risk would be of significance for the management of water resources.