Samples of groundwater were collected during a post-monsoon period (January) and a pre-monsoon period (May) in 2020 from 30 locations in the rapidly developing industrial and residential area of the Coimbatore region in southern India. These sampling periods coincided with times before and during the lockdown in industrial activity and reduced agricultural activity that occurred in the region due to the COVID-19 pandemic. This provided a unique opportunity to evaluate the effects of reduced anthropogenic activity on groundwater quality. Approximately 17% of the wells affected by high fluoride concentrations in the post-monsoon period returned to levels suitable for human consumption in samples collected in the pre-monsoon period. This was probably due to ion exchange processes, infiltration of rainwater during the seasonal monsoon that diluted concentrations of ions including geogenic fluoride, as well as a reduction in anthropogenic inputs during the lockdown. The total hazard index for fluoride in the post-monsoon samples calculated for children, adult women, and adult men indicated that 73%, 60%, and 50% of the groundwater samples, respectively, had fluoride levels higher than the permissible limit. In this study, nitrate pollution declined by 33.4% by the pre-monsoon period relative to the post-monsoon period. The chemical facies of groundwater reverted from the Na-HCO3-Cl and Na–Cl to the Ca-HCO3 type in pre-monsoon samples. Various geogenic indicators like molar ratios, inter-ionic relations along with graphical tools demonstrated that plagioclase mineral weathering, carbonate dissolution, reverse ion exchange, and anthropogenic inputs are influencing the groundwater chemistry of this region. These findings were further supported by the saturation index assessed for the post- and pre-monsoon samples. COVID-19 lockdown considerably reduced groundwater pollution by Na+, K+, Cl–, NO3¯, and F– ions due to shutdown of industries and reduced agricultural activities. Further groundwater quality improvement during lockdown period there is evidence that the COVID-19 lockdown by increased HCO3¯ ion concentration. Overall results illustrate the positive benefits to groundwater quality that could occur as a result of measures to control anthropogenic inputs of pollutants.