Fishways are the main type of hydraulic devices currently used to facilitate migration of fish past obstructions (dams, waterfalls, rapids,…) in rivers. In this paper we present a mathematical formulation of an optimal control problem related to the optimal management of a vertical slot fishway, where the state system is given by the shallow water equations, the control is the flux of inflow water, and the cost function reflects the need of rest areas for fish and of a water velocity suitable for fish leaping and swimming capabilities. We give a first-order optimality condition for characterizing the optimal solutions of this problem. From a numerical point of view, we use a characteristic-Galerkin method for solving the shallow water equations, and we use an optimization algorithm for the computation of the optimal control. Finally, we present numerical results obtained for the realistic case of a standard nine pools fishway.