Massive and excessive use of nitrogen fertilizers and sustained irrigation have been widely practiced in recent years. This strategy leads to a large transfer of nitrates to groundwater, leading to a major environmental problem of nitrate contamination in water, intended for drinking water consumption. One of the most effective solutions is the degradation of nitrites and nitrates, into gaseous nitrogen, using the heterotrophic bacteria during the denitrification process. In this paper, we present and study a mathematical model of the biodenitrification process taking into account the fixed and mobile bacteria. This process is modeled by a system of ordinary differential equations and requires the success of bacteria to colonize the reactor. We study the existence and the asymptotic behaviour of the solution. We show the existence of a value of the injected carbon concentration from which we ensure the success of the biodenitrification process and we propose a heuristic algorithm which serves to control the biodenitrification process over time. Finally, we present some numerical simulations in to support the theoretical results.