In order to study the occurrence form, vertical migration and transformation and the potential ecological risk of Hg in the disjointed hyporheic zone in the gold mining area is investigated. Through field investigation, in-situ test, and test analysis, the results show that: (1) the form of mercury in the original stratum where the river water-groundwater hydraulic connection is disconnected is mainly in the residual state, accounting for 77.78% of the total mercury; (2) after the water content increases or the water level changes, the various forms of occurrence in the soil surface layer decrease, and the residual state is still the main form; the main forms of mercury in the sand and pebble layer are diversified, including the residual state, strong organic state and humic acid state; (3) the mercury content in the subsurface zone in winter is higher than that in summer; (4) although the mercury content in groundwater has not been detected, the potential ecological risk of mercury in the disjointed Hyporheic zone near the river in the study area is much higher than the extreme ecological hazard threshold, which has a value of 320. The risk of groundwater pollution caused by mercury during the long-term runoff of the river is higher than that during the flood period. Therefore, relevant departments need to rectify the river as soon as possible, from the source to reduce the ecological risk of heavy metals to groundwater. The results will provide a scientific basis for groundwater control.