Soil salinization has become a widespread problem that seriously affects the sustainable development of agriculture. To deal with the salt accumulation and leaching problems in practical agricultural systems, a new soil water and solute transport model adopting the mass balance scheme is developed in this study. The soil water movement module is based on a previously published soil water mass balance model, named as UBMOD. The mobile-immobile assumption has been adopted to develop the soil solute transport module, which can describe the obvious anomalous transport phenomenon in practice. The advection, chemical reactions of solute, solute transfer between the mobile and immobile regions, and dispersion in the mobile region are considered in the solute transport module, while only chemical reactions and solute transfer between the mobile and immobile regions are considered in the immobile region. Three cases were designed to evaluate the performance of the model by comparing the simulation results with those obtained by experimental results, HYDRUS-1D, and practical observations. The results demonstrate that the developed model can solve the homogeneous and heterogeneous soil water movement and solute transport effectively, and it has looser restrictions on the discretization of space and time than the numerical solution of Richards’ equation and can keep the mass balance well, which make it more suitable for practical conditions. Moreover, the real-world application of salt accumulation and leaching problems in Hetao Irrigation District, Inner Mongolia, China shows that the RMSE of the simulated soil salt content with the immobile present region is about 20% better than that when ignoring the immobile present region. Therefore, it is necessary to take the significant anomalous transport into account when studying the salt accumulation and leaching processes in practical agricultural systems.