The arsenic concentration in groundwater varies significantly with time and space in groundwater‐surface water exchange zones. Various processes have been identified that control arsenic concentration distribution and mobility in laboratory systems. However, it is still challenging to identify important processes controlling arsenic concentration distribution at the field scale due to the complex coupling of hydrobiogeochemical processes. In this study, a reactive flow and transport model was used to identify dominant processes controlling arsenic distribution and seasonal variations in groundwater‐surface water exchange zones using Jianghan Plain, China, as an example. The results revealed the importance of river water and groundwater interactions on seasonal changes in arsenic concentration; however, the affected region is limited to within 50‐m distance to the river. The modeling results, unexpectedly, revealed the predominant importance of groundwater extraction to the seasonal variation in arsenic concentration. The groundwater extraction changed the groundwater flow pattern and induced vertical leakage of oxygen‐containing surface water into the aquifer, which triggered a series of biogeochemical reactions that changed groundwater redox conditions and promoted arsenic sorption, resulting in a rapid decrease in arsenic concentrations in groundwater. After groundwater extraction ceased, aquifer recovered to anoxic condition, promoting arsenic release from the sorbed phase, leading to a rapid rebounding in groundwater arsenic concentrations. Overall, this study provided a tool to identify coupled hydrobiogeochemical processes on arsenic spatiotemporal distribution and migration in groundwater.