This paper describes an attempt to estimate the mass budget of irrigation ponds within a watershed and the possibilities to control the effluent load of nutrients from the watershed located in the Kyotanabe area. The paddy field lots were irrigated by the ponds and several mountain streams. In the study watershed, there were two ponds located on the upper and lower sides of a paddy area. Water could be pumped up from the lower pond to the upper pond as necessary. At the ponds, the total amount of nitrogen and phosphorus in the inflow loads including the sediment release was larger than those in the outflow loads. In SS, the effect of load reduction in the ponds was high. It is assumed that organic load reduction was not expected in the ponds. The study result indicates that it is possible to remove the nutrients in the ponds when a larger amount of water is pumped up than when the ponds are only in irrigation use. Moreover, the removal capacities of the nutrients could probably be increased in both ponds by controlling the amount of sediment releases.