In semi-arid regions like Rajasthan, groundwater is the largest freshwater source available to the population; because surface water is often limited and seasonal, most households will rely on their groundwater resources for various purposes: domestic, agriculture, and industry. The increasing population, application of fertilizers, growth of urban areas, and natural geochemical processes negatively affect the quality of groundwater in Bharatpur District. Our study evaluates the groundwater quality of Bharatpur District and variation in this quality by seasonally assessing several hydrologic factors: pH, electrical conductivity (EC), total dissolved solids (TDS), total hardness, fluoride concentration, and nitrate concentration. We evaluated the differences in the hydrologic factors among the three identified seasons: pre-monsoon (dry), monsoon (wet), and post-monsoon (dry) seasons. Our results indicate significant differences in the quality (i.e., hydrologic factors) of groundwater across the spatial and temporal scales evaluated; while monsoon rainfall temporarily percolates through to recharge groundwater supplies, the effect is short-lived. Once the monsoon rains cease, and as a result of pollutant mobilization, groundwater quality is significantly reduced in the post-monsoon seasons. Moreover, fluoride and nitrate concentrations will frequently exceed the WHO and BIS permissible limits; when ingested, this can elevate the risk of health issues (fluorosis and methemoglobinemia). Our findings support the ongoing need to monitor and manage future groundwater supplies sustainably.