Introduced largemouth bass (Micropterus salmoides spp.) and bluegill (Lepomis macrochirus spp.) are thought to threaten native aquatic organisms worldwide and hence their eradication has recently begun in Japan. Our previous studies suggested that the removal of largemouth bass increases native fish, shrimp, dragonflies, and exotic crayfish, but decreases macrophytes. To test this prediction, we removed the exotic fishes by draining farm ponds and compared the numbers of these organisms before and after the drain, as well as between drained and undrained ponds. The number of dragonfly Pseudothemis zonata, crayfish, shrimp, and goby increased rapidly after the drain, but the coverage of macrophyte declined. The reduction in macrophyte is assumed to be caused by increased herbivory by crayfish. The number of exuviae of damselfly Cercion calamorum and the total number of species of odonate also decreased after the drain. These decreases can be due to the reduction of macrophyte because reduced odonate species are known to use macrophytes as oviposition sites. Therefore, the removal of largemouth bass has a potential to cause negative effects on some native organisms. We propose that reduction of exotic crayfish should be considered when eradicating the exotic fishes.