Fluoride and nitrate contamination in groundwater is a global concern due to their toxicity and associated negative health effects. This study incorporated a comprehensive methodology, including hydrogeochemical analysis, drinking and irrigation water quality assessment, source apportionment, and health risk estimation of groundwater fluoride and nitrate in a lithium ore deposit basin in western Serbia. Groundwater major ion hydrogeochemistry was governed by water–rock interactions, with Ca-Mg-HCO3 identified as the predominant groundwater type. The entropy-weighted water quality index (EWQI), sodium adsorption ratio (SAR), and sodium percentage (%Na) revealed that 95% of the samples were of excellent to good quality for both drinking and irrigation. Moreover, the results showed that fluorides were of geogenic origin, whereas nitrates originated from agricultural activities. Although the fluoride and nitrate levels in groundwater were relatively low, averaging 1.0 mg/L and 11.1 mg/L, respectively, the results of the health risk assessment revealed that the ingestion of such groundwater can still lead to non-cancerous diseases. The threshold of one for the hazard index was exceeded in 15% and 35% of the samples for adults and children, respectively. Children were more vulnerable to non-carcinogenic risk, with fluorides being the primary contributing factor. The study outcomes can serve as a reference for other lithium-bearing ore areas and guide the management of regional groundwater resources.