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Fish need to make different responses to different water flow conditions, as a variety of fish utilize or overcome the water flow while fish are in the water. This study aims to analyze the response of two types of carp (black carp and silver carp) to water flow in different body lengths (2.0–10.0 cm) in early developmental stages in an open channel. By analyzing the water velocity and fish swimming behavior, swimming against the water flow was the most frequent swimming behavior, and the frequencies of this behavior increased with the increased body length of fish. The results demonstrated that the detectable water velocity of two carp species of different body lengths remained in a certain range (0.020–0.060 m/s). Black carp and silver carp can swim against the water flow of 0.295–0.790 m/s and 0.245–0.825 m/s, respectively. The results of this study can provide invaluable data for engineers and biologists to protect fish in the early developmental stage and restore the ecological habitats in the regulated river systems.