Unit load factor, which is used for the quantification of non-point pollution in watersheds, has the limitation that it does not reflect spatial characteristics of soil, topography and temporal change due to the interannual or seasonal variability of precipitation. Therefore, we developed the method to estimate a watershed-scale non-point pollutant load using seasonal forecast data that forecast changes of precipitation up to 6 months from present time for watershed-scale water quality management. To establish a preemptive countermeasure against non-point pollution sources, it is possible to consider the unstructured management plan which is possible over several months timescale. Notably, it is possible to apply various management methods such as control of sowing and irrigation timing, control of irrigation through water management, and control of fertilizer through fertilization management. In this study, APEX-Paddy model, which can consider the farming method in field scale, was applied to evaluate the applicability of seasonal forecast data. It was confirmed that the rainfall amount during the growing season is an essential factor in the non-point pollution pollutant load. The APEX-Paddy model for quantifying non-point pollution according to various farming methods in paddy fields simulated similarly the annual variation tendency of TN and TP pollutant loads in rice paddies but showed a tendency to underestimate load quantitatively.