The Source-Sink Term (SST) in nitrate (NO-3-N) Convection-Dispersion Equation (CDE), which integrates NO-3-N transport and transformation processes in soils, is affected by considerably complicated micro-environmental conditions and difficult to be measured directly, especially in the field. In this study, the NO-3-N CDE with an unknown SST was solved iteratively with an inverse method to estimate the average SST distribution. The required input information can be easily obtained, including soil hydraulic properties, two successively measured NO-3-N concentration profiles, the boundary and initial conditions etc. Several numerical experiments were designed to examine the accuracy and stability of the inverse approach, considering spatial intervals of the measurement points along the soil profile, time intervals between the successive measurements of soil NO-3-N content, boundary conditions, soil heterogeneity, soil hydraulic properties, and hydrodynamic dispersion coefficient. Compared with the theoretical values, the results showed that the inverse method was reliable for estimating the SST in CDE. An example was employed to demonstrate the application of the inverse method. Based on the estimated distribution of SST, the root-nitrate-uptake (RNU) rate profile was calculated when other parameters in SST model had been determined, and the RNU factor in the RNU model was optimized successfully, when the root-water-uptake (RWU) model was set up or on the occasion the RWU parameters and the root length density information were unknown but two successively measured soil water content profiles were provided.