The present study aims to investigate the spatial distribution and associated various geochemical mechanisms responsible for fluoride (F⁻) contamination in groundwater of unconfined aquifer system along major rivers in Sindh and Punjab, Pakistan. The concentration of F⁻ in groundwater samples ranged from 0.1 to 3.9 mg/L (mean = 1.0 mg/L) in Sindh and 0.1–10.3 mg/L (mean = 1.0 mg/L) in Punjab, respectively with 28.9% and 26.6% of samples exhibited F⁻ contamination beyond WHO permissible limit value (1.5 mg/L). The geochemical processes regulated F⁻ concentration in unconfined aquifer mainly in Sindh and Punjab were categorized as follows: 1) minerals weathering that observed as the key process to control groundwater chemistry in the study areas, 2) the strong correlation between F⁻ and alkaline pH, which provided favorable environmental conditions to promote F⁻ leaching through desperation or by ion exchange process, 3) the 72.6% of samples from Sindh and Punjab were dominated by Na⁺- Cl⁻ type of water, confirmed that the halite dissolution process was the major contributor for F⁻ enrichment in groundwater, 4) dolomite dissolution was main process frequently observed in Sindh, compared with Punjab, 5) the arid climatic conditions promote evaporation process or dissolution of evaporites or both were contributing to the formation of saline groundwater in the study area, 6) the positive correlation observed between elevated F⁻ and fluorite also suggested that the fluorite dissolution also played significant role for leaching of F⁻ in groundwater from sediments, and 7) calcite controlled Ca²⁺ level and enhanced the dissolution of F-bearing minerals and drive F⁻ concentration in groundwater. In a nut shell, this study revealed the worst scenarios of F⁻ contamination via various possible geochemical mechanisms in groundwater along major rivers in Sindh and Punjab, Pakistan, which need immediate attention of regulatory authorities to avoid future hazardous implications.