Sandy lakes are ecologically vulnerable to anthropogenic and climatic stressors. Although lacustrine groundwater discharge (LGD) is recognized as a crucial component of lake hydrology and nutrient cycling, its specific role in regulating environmental vulnerability in these sensitive ecosystems remains poorly quantified. This study employed an integrated approach, combining hydrochemical analysis, water source identification, and a radon (222Rn) isotope mass balance model, to investigate the sources and drivers of major pollutants in saline-salt lakes of the Mu Us Sandy Land. Particular emphasis was placed on the impact of LGD on lake water (LW) quality. The enrichment of nitrogen substances and Mg2+ represented the primary environmental issue within the watershed. Total nitrogen (TN), primarily derived from manure application, and total phosphorus (TP), originating from industrial activities, were identified as the major pollutants of groundwater (GW) and LW. Spatially, saline lakes exhibited better water quality than salt lakes, and lakes in the upper and middle reaches generally had better quality than those downstream. Temporally, water quality variations were closely linked to changes in lake surface area, which were predominantly controlled by precipitation-the primary source of lake recharge, accounting for 65.6% of total inflow. The concentration of 222Rn decreased progressively from GW to porewater and then to LW (2030.17, 1477.41, and 40.61 Bq/m3, respectively), indicating active LGD processes, with a mean LGD rate of 63.60 mm/d within the watershed. This process delivered fluxes of 1.88, 7.92, and 3.18 g/m2/ d for TN, NO3-, and Mg2+, respectively, facilitating their accumulation in the lakes. The ratio of GW input height to lake depth revealed that shallower lakes received a greater proportion of water and nutrient inputs via LGD and consequently exhibited poorer water quality, highlighting the substantial regulatory role of LGD on lake environments. Random forest analysis further indicated that mitigation strategies should target the root causes, namely, industrial/agricultural pollution sources and the LGD pathway. Controlling inputs from these terrestrial sources is therefore essential to reduce pollutant loading in GW and limit their influx into lakes.