Fluoride (F-) and nitrate (NO3-) are main pollutants that significantly impact water quality and human health. However, the spatio-temporal variability of F-and NO3-fate in sandy-land lake group basins remains poorly understood. To address this knowledge gap, we analyzed the spatio-temporal variability of F-and NO3-fate in a representative region (Bahannao Lake Group Basin) using self-organizing maps, positive matrix factorization and radon (222Rn) mass balance model. The results indicated that samples could be grouped into six clusters characterized by distinct hydrochemical types and varying concentrations of F-and NO3-. Specifically, F-predominantly originated from fluorite dissolution, which was facilitated by carbonate precipitation and cation exchange processes. In contrast, anthropogenic activities were the primary source of NO3-. Additionally, seasonal variations in F-and NO3-concentrations were influenced by meteorological factors and the alkaline nature of the environment. Lacustrine groundwater discharge (LGD) rates were 26.28 mm/d and 82.33 mm/d during wet and dry season, respectively. Correspondingly, the fluxes of F-and NO3-fluxes transported from groundwater to lakes posed substantial risks to the lake ecosystem. Non-carcinogenic risks associated with F-and NO3-exposure affected 74.5 % of adults and 83.8 % of children, respectively. The methodologies and insights presented in this study enhance our understanding of the genesis and evolution of lake water quality degradation in semi-arid regions.