Hyporheic exchange and nitrogen cycle processes under the dual effects of flooding and heterogeneous streambed

•In-situ experiments were conducted to depict the hydrogeological characteristics of gravelly streambed in the field.•A coupled model of river turbulence-groundwater percolation-solute transport was constructed.•Different simulation schemes were designated using monitored flood processes and stochastic conductivity fields.•The characteristics of hyporheic exchange and nitrogen cycle processes under the dual action of flood and heterogeneous medium were analyzed.