Rice production is one of the major non-point sources of pesticide pollution in Japan. Monitoring of pesticide concentrations in river systems detected a number of herbicides commonly used in paddy fields, and these concentrations may appear to have adverse effects on the aquatic ecosystem. In this paper, two mathematical models developed in Japan, the PADDY and PCPF models for simulating the fate and transport of pesticides in a paddy environment are introduced. These models have been validated with observed data from laboratory experiments and field monitoring studies. In addition, the application of a mathematical model (RICEWQ) modified in Europe for high tier risk assessment in paddies is provided. We applied the PADDY and PCPF models to controlling pesticide runoff losses from paddy fields and to ecological risk assessment in the aquatic environment. The recommendation from model simulations for reducing pesticide runoff from paddy fields are 1) application of an intermittent irrigation scheme with a high drainage gate and 2) application of a longer water holding period after pesticide application. In order to establish a realistic assessment and management procedure for environmentally-friendly rice production, it is important to develop and validate mathematical models adapted to paddies in the Asian region.