Major ions, δ³⁴S_SO4 and δ¹⁸O_SO4 of Zhujiang River in Southeast China were determined to examine the sources of the dissolved loads and the influence of human perturbations and chemical weathering on the water quality and health risk. Ca²⁺ and HCO₃⁻ constitute the majority of major ions, Ca²⁺ contents range from 7.88 to 85.59 mg/L, with an average value of 45.49 mg/L, while the concentrations of HCO₃⁻ vary between 31.02 and 247.71 mg/L. The δ³⁴S_SO4 and δ¹⁸O_SO4 signals vary from − 9.69 to 7.88‰ and 1.55 to 9.32‰, respectively. The analyses including principal component analysis, Piper diagram and the elemental ratios demonstrate that water chemistry is dominated by the carbonate weathering, which is facilitated by sulfuric acid. The mass balance model using δ³⁴S_SO4 and δ¹⁸O_SO4 reveals that the riverine SO₄²⁻ are mainly from the human activities. And in the Xunjiang River and Xijiang River channel located in the lower reaches, Guangdong province with the relatively developed economy compared to the upper reaches, the anthropogenic inputs contribute more to the riverine SO₄²⁻. In comparison with the drinking water guideline, Zhujiang river water is generally suitable for drinking. The sodium hazard assessments for irrigation demonstrate that only one sample with the SAR value of 1.14 and Na% of 30.7% exceeds the desirable limits, indicating long-time use of the water may undermine the structure of soil aggregates and reduce agricultural production, for most sites, the water are suitable for irrigation. The calculated hazard quotient (HQ) including F⁻, NO₃⁻, NH₄⁺ for adults are all within 1, indicating ignorable risk. While in the upper reaches where the acid rain is common, the children are threatened by the non-carcinogenic hazards. The human activities no doubt affect the water quality and increase the health risk for the local residents, thus long-time monitoring on water quality and limiting pollution emissions from sewage and activities should be taken seriously.