This paper systematically summaries the mathematical models of hydrodynamics, solute transport and microbial growth processes, which describe nitrogen transport and transformation behavior in the hyporheic zone, as well as the coupling relationships of these models. The main parameters and influencing factors of the coupled models are analyzed. The influence of experimental data acquisition, process coupling relationship establishment and model parameter identification on the uncertainty of numerical simulation is discussed. In view of the shortcomings of the existing research, it is proposed that more research should be devoted to the original environment monitoring of the hyporheic zone, the coupling of heat transfer process with other processes and the optimization calculation of the multi-dimensional multi-process coupled model in the future.