Seasonal variations in groundwater reveal lesser concentrations of major ions except NO3- during post-monsoon seasons in shallow aquifers as compared to deeper aquifers. The F- concentration from deeper aquifers is high in both seasons and shows a moderate positive relationship with weathering depth and is >5mg/L in compound lava flow. Groundwater is mainly a Ca-HCO3 type in shallow aquifers and mixed type in deeper aquifers. Fluoride shows a positive correlation with pH, Na+, HCO3- in shallow aquifers and an inverse correlation with Ca2+ and HCO3- from deeper aquifers in both seasons. Approximately 45% of the samples are not suitable for drinking from both aquifers but suitable for irrigation purposes. Rock-water interaction, moderate alkalinity, sluggish movement, and higher residence time are the main causes for high F-in deeper aquifers as compared to shallow aquifers. As recommendations, drinking water requirement may be met from shallow aquifers/surface water and fluoride rich groundwater for other purposes. Most effective defluoridation techniques like ion exchange and reverse osmosis may be adopted along with integrated fluorosis mitigation measures and rooftop rainwater harvesting. Supplementary calcium and phosphorous rich food should be provided to children and creating awareness about safe drinking water habits, side effects of high F-, and NO3- rich groundwater, improving oral hygiene conditions are other measures.