Abstract: Water level of the hyporheic zone essentially varies in different hydrological periods. In order to investigate the geochemical characteristics of the lateral hyporheic zone in different hydrological periods, Maanxi Creek in Chongqing was selected to be the study site. The water level, temperature, dissolved oxygen, pH, specific conductance, and selected ions concentrations of the river water, lateral hyporheic zone, and groundwater were monitored during the transitional period of wet season to dry season (October to December). Results show that the water level of the lateral hyporheic zone was changed greatly with the arriving of dry season. The water level gradient decreased between river and hyporheic zone, resulting in a reduction of infiltration from the river water. Because of change of water level and temperature drop of infiltrated water, the microbial activities in the lateral hyporheic zone declined, which increases pH and decreases dissolved oxygen. These changes also reduced the specific conductance and weakened the purification capacity of the lateral hyporheic zone to nitrate and sulfate, and enhanced the fixation capacity to the heavy metals, like manganese and zinc. Based on the analysis of the geochemical dynamics of the hyporheic zone, it can be deduced that the boundary of the hyporheic zone was shifted from a place of 30-50 cm in the wet season to a place of less than 30 cm away from the riverbank in the dry season.