Mining legacies continue to impact the geochemical cycles in historically mined watersheds after mine closure. The Hokuroku District in Northeast Japan is a famous metal mining area with a long mining history; however, studies on the distribution mechanisms and pollution characteristics of heavy metals in these historically mined watersheds after the boom period of mining activities are lacking. This study aims to provide fundamental insights into the effects of the mining activities and hydrological conditions on heavy metal pollution in the Kosaka watershed, Hokuroku District. Sampling was performed in terms of watershed segmentation, and the outlet of the tributary within each sub-watershed was also sampled to capture the diffusional pollution status. The distributions of Zn, Cu, Cd, Pb and As in river water and sediments, as well as their pollution characteristics and ecological risks, were analysed under different hydrological conditions. Our findings provide evidence of the ecological risk in surface water induced by Zn, Cu and Pb pollution in the Kosaka River system. In a high proportion of the sub-watershed, there was moderate to strong enrichment in Cd, Cu and Zn in the river sediments. The sub-watersheds with high pollution levels and ecological risk were highly consistent with the sub-watersheds encompassing abandoned mine sites. Suspended particles carried large amounts of Pb and Cu, especially on rainy days. The heavy metal contents in river water were very sensitive to occasional rainfall events; rainy days posed the most risk to organisms in the Kosaka River, followed by the low-water-level season and the high-water-level season.