Longitudinal river fragmentation through physical barriers is a major issue for the conservation of aquatic species in regions with intense hydropower development, such as Chile. The construction of fishways is the main mitigation strategy for maintaining connectivity for fish but development of designs suitable for a broad range of species is challenging. Recent work has shown that two species native to Chile, Cheirodon galusdae and Basilichthys microlepidotus exhibited similar swimming performance in free flow in the laboratory, indicating that a single fishway design may be suitable for both species. However, in the complex, three-dimensional altered flows observed in fishways, swimming performance is likely to vary from the free flow case due to the adoption of distinctive swimming gaits, variation in swimming styles, and the potentially destabilizing effects of wake vortices. In order to improve criteria for hydraulic design of fishways for multiple species we study the behavior and tail beat kinematics of C. galusdae and B. microlepidotus (juveniles), in the wake of vertical and bottom-mounted cylinders in an open channel flow. Cheirodon galusdae swam using a burst-and-coast style. This species avoided the cylinder wakes, searching for more favorable flow conditions. Basilichthys microlepidotus adopted a Karman gait-like swimming strategy to swim in the cylinder wake. Tail beat frequency was constant in all experiments for both species, but in the presence of cylinders >2 cm in diameter, C. galusdae diminished the duration of the coast phase evidencing a higher propulsive effort. Tail beat amplitude of both species increased with the vortex length scale and decreased linearly with vortex shedding frequency. The fish Strouhal number correlated well with the relative vortex size and shedding frequency, compiling the swimming effort of species with very different behaviors, indicating that it is a suitable criterion for fishway design. (C) 2017 Elsevier B.V. All rights reserved.