A model in which a river model was layered on a distributed model (double-layered model) was developed to analyse the transport of water and pollutants (nitrogen, phosphorus, and BOD as organic matter) in watersheds and rivers. The model was applied to the watershed of Abragafuchi Lake, Japan, where serious water pollution has occurred over three decades, and the applicability of the model was demonstrated. Scenarios of recycling of sewage treated-water into agriculture to reduce pollutant load discharged into the lake were analysed. The results showed that irrigating paddy fields with the sewage-treated water could contribute to conserving water and reducing pollutant load, with reduction rate in BOD, nitrogen, and phosphorus ranging from 6%-36%, 16%-46%, and 18%-51%, respectively. Particularly, the results indicated that, irrigating paddy fields with the treated water during non-cropping periods and the accompanying reduction in withdrawn water from the river were more effective in reducing pollutant loads discharged into the lake. Further study is required on the effect of recycled water on crop cultivation and soil conditions for safe implementation.