In the present study, the effects of muddy water were compared and examined on the fish inhabiting Imha reservoir, E. erythropterus, H. labeo and Z. platypus in Cypriniformes, S. asotus in Siluriformes and S. scherzeri in Perciformes. In the gills of fish in muddy water, the secondary lamellae of fish in Cypriniformes showed more irregular gaps and more winding than those in Siluriformes and Perciformes. Also, the edema and detachment of epithelial cells was more detected in the gills in Cypriniformes, but clubbing was frequently detected in Perciformes and Siluriformes. Also, we found that muddy debris and minute particles attached to lamellae were frequently detected in Perciformes and Cypriniformes. The glomerulus in the kidney was much more constricted in Z. platypus in Cypriniformes. As a result, it is proposed that fish in Cypriniformes are more affected by muddy water. In the changes of blood components, which might be affected by muddy water, the concentrations of TP, ALB, TG, CHOL and A/G ratio, were high in Cypriniformes, and inorganic matters were abundant in Siluriformes. In addition, AST activity was relatively higher than ALT and both activities were higher in Cypriniformes than in Siluriformes. Taken together, the change in blood plasma may be caused by the reduction in voracity in the wake of muddy water, which results in tissue damage.