The groundwater quality degradation is due to agriculture, industrial and domestic activities; thus, sustainable management of available water resources becomes the need of the hour in arid and semi-arid regions. Therefore, the present study aims to find the source, occurrence, controlling factors and exposure risk of fluoride (F) and boron (B) contaminations in the groundwater of basaltic geology of the semi-arid region of Maharashtra. For this purpose, 68 representative groundwater samples from shallow aquifers were collected and analysed for major ions to find the geochemistry in relation to B and F. The chemical analysis revealed that F and B contents in the drinking water are above the threshold level of the WHO; hence, the health risk to infants, children and adults is assessed by computing ADD, HQ and THI values. HQ values of F depicted that children have high risk followed by adults and infants, and they possess moderated non-carcinogenic risk in both seasons. HQ values of B inferred that infants are more susceptible than adults. THI confirms that children (52.94%), adults (35.29%) and infants (8.82%) possess non-carcinogenic risk in the pre-monsoon season and 32.35% children and 23.52% adults possess non-carcinogenic risk because of (THI > 1) in the post-monsoon season. The outcomes of the study advocated that children are posing a higher non-carcinogenic risk as compared to adults and infants in both the seasons. Therefore, it is essential to take precautionary measures to avoid any health problems by implementing appropriate measures. Also, continuous monitoring of F and B levels in groundwater and its removal techniques are recommended to diminish the potential health hazards.