A jet fish pump with a throat of ø60mm was designed to study its performance in the transport of different fish species and the physiological changes in fish thereafter. Experiments were conducted to investigate the fish transport rate and energy required to transport each ton of fish when transporting Carassius auratus, commonly known as the Chinese goldfish, Megalobrama amblycephala, or Wuchang bream, and Ctenopharyngodon idella, the grass carp. Fish were examined for external injuries as well as for several important enzymes and hormones which are indicators of tissue injury and stress. The results showed that the transport rate for all three species of fish rose dramatically with an increase in the primary stream rate. In this experiment, the transport rates of C. auratus, M. amblycephala and C. idella reached 2357±37.2kg∙h−1, 2888±41.6kg∙h−1, and 2060±40.2kg∙h−1, respectively. However, both injury rate and energy required to transport each ton of fish increased no matter whether the primary stream rate was too low or too high. Considering both transport rate and injury rate, the mean primary stream rate of 80m3∙h−1 was determined to be the optimal operating condition in this experiment. Fish were stressed and most likely some of their organs were damaged. However, most physiological indexes almost fully recovered after several hours.