A physical model was developed to describe the soil-to-stream export processes of water and pollutants in a small river basin during the soil thawing period. The hydrological and pollution transport and transformation behaviors in paddy- and corn-dominated catchments were numerically simulated; the impacts of the pollution concentrations, interactions between the migrated water and pollutants in the soil, and pollutant transformations during the pollution export were coupled. Experimental field data from the Heidingzi river basin during the soil thawing period were used to calibrate the model parameters and evaluate the performance. The mass of the dissolved pollutants from soil particles in the migrated soil pore water was the key factor affecting the pollution export into the streams; the water content directly affected the pollution export. The concentration of the pollutants peaked when the initial exported water was high. The pollutant transport processes influenced the pollution export more significantly after the soil water was significantly reduced. The N-S efficiency coefficients between the simulated and monitored flow rates and the pollution concentrations at the outlets of the paddy- and corn-dominated catchments were >0.60 and >0.54, respectively. The system deviations between the simulated and monitored flow rates and the pollution concentrations were <10% and <15%, respectively. The proposed model effectively described the water flow, pollution transport and transformation processes