Nitrogen and phosphorus concentrations and temporal variations were investigated in the Shin and the Kasuga rivers, Shikoku Island, Japan. For effective water-use, many irrigation ponds were located in these river basins, and many weirs were established in the rivers themselves. Our investigation was carried out in waters dammed up by river mouth weirs in both rivers. TN and TP concentrations were high, reaching values of 7.35 mg L and 0.505 mg L-1, respectively. TN concentrations were comparatively low from spring to autumn during the irrigation period. In this season, the dilution effect of irrigation water with a low TN concentration from the Yoshino River had to be considered. The proportions of organic nitrogen and phosphorus in both TN and TP were high in both rivers. The organic nitrogen and phosphorus especially increased in winter during low water temperatures. Precipitation and the water supply from the Kagawa water canal were low in this period, and the volume of river water markedly decreased. It was indicated that the organic substance production rose by the increase in the residence time of the water. In addition, the inflow of organic material to the river by the draining of pond water for pond bottom improvement was also considered as a factor in high levels of organic material in the river. © 2011, The Japanese Society of Limnology. All rights reserved.