Three-dimensional numerical simulations were performed for different flow rates and various geometrical parameters of step-pools in steep open channels to gain insight into the occurrence of energy loss and its dependence on the flow structure. For a given channel with step-pools, energy loss varied only marginally with increasing flow rate in the nappe and transition flow regimes, while it increased in the skimming regime. Energy loss is positively correlated with the size of the recirculation zone, velocity in the recirculation zone and the vorticity. For the same flow rate, energy loss increased by 31.6% when the horizontal face inclination increased from 2◦ to 10◦, while it decreased by 58.6% when the vertical face inclination increased from 40◦ to 70◦ . In a channel with several step-pools, cumulative energy loss is linearly related to the number of step-pools, for nappe and transition flows. However, it is a nonlinear function for skimming flows. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.