This paper is devoted to modelling of water flow dynamics in open-channels for the goal of controlling irrigation systems. We expose and validate a methodology based on Lattice Boltzmann models as an alternative to the commonly used Saint-Venant equations. We adapt a bi-fluid model to the case of a free surface water flow. A gravity force is applied to the heaviest fluid as to maintain it at the bottom. The considered boundary conditions take into account the control actions provided by the two underflow gates located at the left and right ends of the reach. Numerical results for density profiles are given to validate our approach.