Most dams planned for construction on large Neotropical rivers must have fishways if the migratory fish resources are to conserved. In general, these warm productive rivers have many migratory fish species, great fish abundance, and almost nothing is known about fish behavior or swimming ability. To pass fish around dams 30 m high in these rivers, some type of bypass will often be the best choice. However, an innovation bypass design is required due to the need for combining energy dissipation within the bypass with sufficient attraction water for surface-and bottom-oriented fishes (characiformes and Siluriformes are the dominant orders of fish in the Neotropics). This is the situation at two new 3 GW dams (20-25 m head) being built in Brazil on the Madeira River, a tributary of the middle Amazon River, where there are about 700 fish species and great fish abundance. A conceptual model using a scientific approach with several key phases leading to selection of the structure-flow design for a channel bypass (CB) follows: (1) form a Fish Passage Team composed of one or more hydraulic engineers and fish behaviorists with fish passage experience, (2) use small-scale hydraulic models to identify potential structure-flow design with low turbulence and good energy dissipation, (3) scale-up the best structure-flow designs in a large flume and measure their hydraulics, (4) test fish in each design using modern technology to observe fish passage success, swimming speed, and behavior of target species, and (5) identify the best structure-flow CB design based on data from design hyrdaulics and fish performance. This five-step conceptual model identifies the CB design that best passes local fishes and reduces the probability for failure of a fishway design.