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In September 2013, Typhoon Man-yi (known as Typhoon No.18 in Japan) brought heavy rainfall in Shiga Prefecture, Japan, and caused fluvial flood along the Kamogawa River basin in Takashima city and the Daidogawa River basin in Koka city. In particular, the right bank of Kamogawa River was collapsed in the town of Miyano in Takashima city and the flood water inundated a large number of rice paddies which provide habitats for various aquatic organisms. In 2015 and 2016, distributional surveys of the large branchiopod crustaceans of rice paddies in the inundated area were conducted and compared with the results before the flood. Branchinella kugenumaensis (Ishikawa) and Eulimnadia sp. were found at the rice paddies near the collapsed point of Kamogawa River, and Caenestheriella gifuensis (Ishikawa) was found in the inundated area of Kamogawa flooding. On the other hand, C. gifuensis was widely distributed along the Daidogawa River basin in Koka city, and B. kugenumaensis, Leptestheria kawachiensis (Ueno) and Eulimnadia sp. expanded their habitats in the inundated area of Daidogawa flooding. Species co-occurrence, occurrence relative to paddy soils and the types of irrigation and drainage systems are also discussed.