A Genetic Algorithm technique, linked with a numerical solver model (Finite Elements) (GA-FEM), has been evolved to compute the optimal hydraulic design for a safe hydraulic structure to handle seepage concerns. The minimum cost of construction was considered the objective function during the formulation of the optimization process. While the major constraints were represented by the uplift pressure beneath the base floor and the exit gradient of seepage flow. The GA-FEM approach proposed in this study addresses the criteria of optimal hydraulic design in two main steps. First, the seepage problem was analyzed using a verified numerical model coded in finite-element programming. Then the Genetic Algorithm technique is used to address the optimal solution model and obtain the optimum (minimum construction costs) location and depth for the cut-offs under hydraulic structures. As a simulation/optimization (S–O) model, MATLAB platform code was utilized to construct a connection between the FEM and the optimization technique. The results refer to the developed GA-FEM model that can yield efficient, economical, and safe hydraulic designs for the cut-offs. The assessment of the GA-FEM proposed model indicated a good agreement between the simulation and expected results for seepage characteristics under the hydraulic structure.