Abstract: The transport and transformation processes of non-point source pollutions form paddy rice field to the main drainage canal through lateral and branch drainage canals were monitored in the Qianguo irrigation district during the rice growing seasons in 2009 and 2010. Water balance were measured in lateral canal in the controlled irrigation region. Results showed that the drainage water were composed of the rice field surface returned water, the irrigation returned water and the seepage from rice field to the drainage canals. Drainage processes in branch and main canal were simulated using the Muskingum method and the Muskingum segmentation flow routing method, respectively. The transport processes of chemical concentrations were determined by the mix and convection of water flow and the transformation processes were described using the first order kinetic equation. Drainage processes and contaminant concentration simulated showed good agreements with the measured values. The returned water and seepage from rice field played key roles in the process of agricultural non point pollution into the river. This research suggested the surface drainage and seepage water contributed to the non-point source pollution in the paddy irrigation district.