A restored riparian zone was characterized to understand the effects of flooding on subsurface hydrological flow paths and nitrate removal in groundwater. Field and laboratory investigations were combined with numerical modeling of dynamic flow and reactive nitrate transport. Flooding enhances nitrate removal in groundwater primarily by two mechanisms. First, by creating a stagnant flow zone beneath the flooded area thereby increasing the residence time and leaving more time for nitrate removal. Secondly, nitrate removal is increased by enhancing upward flow into the highly reactive organic-rich top layers. Flooding therefore contributes to nitrate removal in "hot spots", where nitrate is transported to the peat and during "hot moments", when flow is stagnant. The permeability of the capping peat layer relative to the aquifer is important as it controls both mechanisms. The model shows that the deep-seated nitrate removal is greater than projected from the laboratory nitrate reduction experiments.