Abstract: River-bed clogging caused by biological agent is a common phenomenon and affected by many environment factors. But bioclogging was rarely considered when studying the nitrogen cycle in hyporheic zone. It establishes a numerical model by simultaneously coupling water flow, reactive transport of solutes and microbial growth, to simulate the hyporheic exchange driven by an undulate river bed and explore the effect of bioclogging. The~present study showed that bioclogging promotes the development of a low permeability layer and high biomass in superficial zone of dunes. Bioclogging limits the spatial distribution of NO3- and results in NH4+ contamination in hyporheic zone. The abundance of organic carbon in river enhances bioclogging extent, which improves the rates of denitrification to remove NO3-. The more fluctuated river bed surface and the larger surface water flow would increase pressure gradient along bed-dunes, bioclogging range and bacterial biomass, then the reaction rates of nitrification and denitrification. It is helpful for the removal of NO3- and NH4+. The bioclogging is beneficial to remove nitrogen pollutants in hyporheic zone and is affected at pressure gradient along bed-dunes, as well as biomass of heterotrophic~bacteria.