The forecasted increase in electricity demand presents challenges due to the desire for renewable generation with minimal environmental impact. In this context, small-scale hydroelectric plants represent a viable alternative to traditional generation methods. This paper presents the design of a water level controller based on differential flatness, applied to a small-scale hydroelectric plant, with the aim of using water efficiently. The dynamic model of the system resembles that of a two-tank system, which exhibits the property of differential flatness. Leveraging this property, its representation in terms of differential flatness is developed, facilitating the controller’s design. Two case studies are presented through computer simulation, in which the system must follow reference trajectories and is subject to operational constraints, with the aim of validating the proposed control scheme. In the first case study, the regulation of the water level in the head tank is addressed, while in the second, the objective is to regulate the water level in the surge tank.