The factors causing water pollution in a basin with scarce water resources was studied in Kagawa Prefecture. The research was conducted in the Shin River basin, which is one of the main basins in Kagawa Prefecture, on October 23, 2010 during the non-irrigation season and on July 16, 2011 during the irrigation season. During the non-irrigation season when the quantity of river water decreased, the number of algal cells increased to 2.3×10
4−7.8×10
4 cells mL
-1 in accordance with the increase in the concentration in irrigation ponds, and species composition changed to
Pseudanabaena sp. as well as irrigation pond. Although
Microcystis sp. was also dominant in the middle/lower reaches as well as the irrigation ponds during the irrigation season when the quantity of river water was relatively abundant, cell numbers were lower than in October. In addition, the number of algal cells in the river correlated well with δ
18O in the river water; irrigation pond phytoplankton is supplied to rivers when water flows from irrigation ponds to the river. The influence of irrigation ponds on rivers was found to increase during non-irrigation seasons when irrigation water is scarce and precipitation is low, and so the quantity of river water decreases.
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