Mercury (Hg) in runoff water poses significant ecological risks to aquatic ecosystems that can affect organisms. However, accurately identifying the sources and transformation processes of Hg in runoff water is challenging due to complex natural conditions. This study provides a comprehensive investigation of Hg dynamics in water from rainfall to runoff. The Hg isotope fractionation in water was characterized, which allows accurate quantification of Hg sources, transport, and transformations in rainfall-runoff processes. Delta 200Hg and corrected Delta 199Hg values can serve as reliable tracers for identifying Hg sources in the runoff water and the variation of delta 202Hg can be explained by Hg transformation processes. During runoff migration processes, Hg from rainfall is rapidly absorbed on the land surface, while terrestrial Hg entering the water by the dissolution process becomes the primary component of dissolved mercury (DHg). Besides the dissolution and adsorption, microbial Hg(II) reduction and demethylation of MeHg were dominant processes for DHg in the runoff water that flows through the rice paddies, while photochemical Hg(II) reduction was the dominant process for DHg in the runoff water with low water exchange rates. Particulate Hg (PHg) in runoff water is dominantly originated by the terrestrial material and derived from the dissolution and adsorption process. Tracking sources and transformations of Hg in runoff water during the rainfall-runoff process provides a basis for studying Hg pollution in larger water bodies under complex environmental factors.