In recent years, the drainage condition of rice fields has been improved for upland crops planting by the farm land consolidation in order to increase farm productivity. On the other hand, the improvement of drainage conditions in paddy field area greatly influenced the habitat of freshwater fishes. However, there are few researches on how freshwater fishes have been influenced by the drainage improvement. In this research, we investigated the difference between the environment for freshwater fishes in drainage canals in the year when the whole area was planted to rice and in the year when a part of the rice field area was planted to wheat. When an upland crop such as wheat was planted in paddy field area, the water depth in the drainage canal among all the environmental components greatly changed. The vegetation on the levees was not available for freshwater fishes due to the fact that the water level in the canal did not increase up to the level of levees, and this drastically decreased the number of fishes living in the canal. Furthermore, from the analysis of the relationship between the number of fishes and the distance from vegetation zone, it could be suggested that at least one vegetation zone of length 100m must be created along the canal with the aim of maintaining the habitat for freshwater fishes.