The riverine magnesium (Mg) isotope composition is generally controlled by sources and fractionation processes. However, it remains unclear in which cases these factors are predominant at the basin scale. In this study, we investigated the major elements, trace elements, and Mg and strontium (Sr) isotope ratios in the Yarlung Tsangpo River (YTR) Basin, southern Tibetan Plateau (TP), to explore the geochemical behavior of Mg isotopes and the dominant controlling factors. Riverine Mg2+ was shown to derive primarily from the weathering of silicates and carbonates. Riverine δ26Mg, which is first influenced by the mixing of different lithological sources, was detected ranging from −1.63 ‰ to −0.52 ‰. According to the saturation indexes of common Mg-bearing secondary minerals, the basin was divided into two zones. Above Shannan City (Zone I), where river waters mostly were oversaturated with minerals, positive correlations were observed between δ26Mg and the Ca/Mg and Sr/Mg ratios. This indicated that, after mixing, secondary minerals (talc and chlorite), which tend to preferentially incorporate 24Mg, may be formed in most of waters, leading to an increase in riverine δ26Mg values. The Rayleigh and batch fractionation models were fitted with factors ranging from 0.9975 to 0.9997. Below Shannan City (Zone II), where river waters mostly were unsaturated with minerals, riverine δ26Mg was positively correlated with 87Sr/86Sr and negatively correlated with the Ca/Mg, Sr/Mg, and HCO3/Na ratios. This suggested that the riverine δ26Mg were influenced by carbonate dissolution with faster kinetic rates. Our analysis of riverine δ26Mg values in the YTR Basin may be a reference for interpreting the relationships between δ26Mg and δ7Li in river systems worldwide. In minerals-oversaturated waters, secondary mineral formation was shown to lead to isotope fractionation, resulting in a positive correlation between the two parameters, whereas in minerals-unsaturated waters, the δ26Mg and δ7Li values were negatively correlated, possibly due to the predominance of mineral dissolution.