Unlike in nonregulated rivers, new ecological filters are formed in artificial reservoirs: structures (gradient zones between biotopes) which affect the behavior and distribution of juvenile fish and therefore change parameters of the downstream migration. One distinct feature of such filters is their selective effect on different species and age groups of migrants when they pass boundaries between biotopes. The differential transparency of boundaries considerably affects the composition of migrants and dispersal of juvenile fish over biotopes. These suggestions are confirmed by the data of long-term studies on the downstream migration of juvenile Cyprinidae and Percidae in several reservoirs in Eurasia: Sheksna (Sheksna River), Ivankovo (Volga River), Kapchagay (Ili River), and Sarez (Murghab River) Reservoirs. The formation of ecological filters is shown in the zone of wedging-out backwaters (lotic–limnetic transformation) and in the zone between the littoral (resident) and pelagic (migratory) biotopes in the reservoir and in the near-dam broads. Emigration of juveniles from the reservoir depends on the location of the water intake (deep-water or surface) and overlapping of water intake zones with those of the spatial distribution of juvenile fish. The different selectivity of water intake sites of the hydroelectric power station located not far from each other and of a navigation lock forms different (in species and age composition) complexes of emigrants. The mechanisms and consequences of functioning ecological filters and ecological barriers are considered.