As the largest and most representative tributary of the Mekong River, the Mun River Basin (MRB) provides critical understanding of regional hydro-geochemical features and rock weathering processes on a basin scale. The present study measured strontium (Sr) isotopes with hydro-geochemistry data of 56 water samples in detail in the MRB in northeast Thailand. The dissolved Sr contents and 87Sr/86Sr isotopic ratios were reported to be 8.7–344.6 μg/L (average 126.9 μg/L) and 0.7085–0.7281 (average 0.7156), respectively. The concentrations of dissolved Sr in the mainstream slightly decreased from upstream to downstream, while the variation trend of 87Sr/86Sr was on the contrary. Correlation analysis showed that Na+ strongly correlated with Cl− (0.995, p < 0.01), while Ca2+ exhibited weak relationships with SO42− (0.356, p < 0.01). Samples of the MRB exhibited lower Mg2+/Na+, Ca2+/Na+, HCO3−/Na+ and 1000Sr/Na ratios, and gathered around the end-member of evaporite dissolution, with slight shift to silicate weathering end-member, demonstrating the dominant contribution of evaporite dissolution and silicate weathering on dissolved loads. Comparing with data of major world rivers from previous research, our results remained consistency with rivers draining through similar geological conditions. The dissolved Sr flux to the adjacent Mekong River was estimated to be 20.7 tons/year. In accordance with the forward model, silicate weathering rate and CO2 consumption rate during dry season were calculated to be 0.73 tons/km2/year and 1.94 × 104 mol/km2/year, and may get underestimated due to intense water consumption by extensive agricultural activities. The superimposed effect of anthropogenic impacts on the water environment could enhance chemical weathering, and thus should be taken into account in regional ion cycles and carbon budgets. These findings highlight the coupling analysis of Sr isotopes and hydro-geochemistry in Earth surface processes and provide basic investigation for sustainable regional water treatment mechanisms in the pan basin of the Mekong River.