Structural solutions in terms of fish ladders and the use of natural materials to construct them often raise concerns regarding the possibility of using the standard calculation methods. The fish ladder being designed on the Wisłok river consists of three pools, separated from each other by baffles made of rock boulders. The purpose of this study was to analyze water surface profiles for fish ladder at specific values of flow rates. The paper presents the results of hydraulic calculations under the conditions of constant flow rate based on the concept of a minimum specific energy. According to this method, water flow through boulders is critical. Thus, it does not take into account head losses, which are hard to estimate and which are the integral part of typical calculation methods, e.g. the use of equations to determine the flow rate of a weir. An additional advantage of this method is that there is no need to assume the flow pattern of one specific weir. Verification calculations of the water depths were conducted using the HEC–RAS software, under an assumption of an one-dimensional steady water flow. Water depths in the fish ladder, calculated using both methods, were similar, despite the adopted different calculation concepts, and can be used in ichthyologic analyses.