The physicochemical properties and heavy metal(loid) concentrations of the river water both fluctuate greatly along the river affected by mining activities, and the transportation of heavy metal(loid)s is therefore more complicated than unpolluted river. Dissolved and particulate heavy metal(loid)s in a river polluted by mining activities were measured to study their temporal-spatial variation and partitioning. The concentrations of dissolved arsenic (As), cadmium (Cd), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) were considerably high at the sites near the mine area. Notably, dissolved As at most sites were higher than the Chinese quality criterion of class II for surface water indicating high environmental risk. Mn and Pb at most sites and Ni at a part of the sites mainly existed in the particulate phase. For other heavy metal(loid)s, i.e., As, Cd, chromium (Cr), and Zn, the particulate phase was extremely high at the sites near the mine area and responsible for heavy metal(loid) transport. Significant correlations between particulate heavy metal(loid)s and temperature and electrical conductivity (EC) were found. However, the partitioning of heavy metal(loid)s did not significantly relate to the river water properties, due to most heavy metal(loid)s in suspended particulate matter (SPM) are stable and affected less by water properties. Except for Cr and Ni, other heavy metal(loid)s showed high concentrations in sediments, and considerable Cd, Mn, and Zn existed in exchangeable and carbonate fraction indicating high environmental risk. The environmental assessment of SPM showed that Cd, Zn, and As, as the main pollutants in SPM, all reached extremely polluted level at the sites near the mine area, and the environmental risk of heavy metal(loid)s in SPM was higher during dry season than that during wet season. The results can contribute to understanding the partitioning and transportation of heavy metal(loid)s in the river affected by mining activities.