Temporal changes in total nitrogen (T-N) and phosphorus (T-P) concentrations in paddy floodwater in response to fertilization under rain-shielding pot and small-scaled field conditions were investigated. On the basis of the changing patterns, suggestions for the use of fertilization factors, such as days after fertilization, in developing models for the estimation of T-N and T-P loads from paddy fields were made. Total N concentration was susceptible to fertilization, showing a peak concentration right after fertilization followed by a decreasing pattern with the elapse of days after fertilization. The decreasing pattern of T-N concentration followed the first- order kinetics, indicating that the models are likely to be an exponential equation using days after fertilization as an independent variable. Comparison between the pot and field experiments conducted with soils different in soil fertility revealed that indigenous soil N concentration significantly affected T-N concentration, and this suggests that soil N status can be used as the second variable for the models. Meanwhile, temporal changes in T-P concentration did not respond to P fertilization as sensitively as T-N. In combination with other published results, our study suggests that rainfall intensity and other factors associated with farming activities that are likely to cause disturbance of soil particles containing P may be used as possible variables for the models.