Past numerical and experimental research has shown that the draft tube inlet velocity is critically important to hydropower plant performance, especially in the case of low-head installations. However, less is known about the influence of flow parameters on turbine performance particularly swirl distribution. Based on the influence of draft tube flow characteristics on the overall performance of a low-head turbine, this research proposes a methodology for optimizing draft tube inlet velocity profiles as a new approach to controlling the flow conditions in order to yield better draft tube and turbine performance. Numerical optimization methods have been used successfully for a variety of design problems. However, addressing the optimization of boundary conditions in hydraulic turbines poses a new challenge. In this paper, three different vortex equations for representing the inlet velocity profile are applied to a cone diffuser, and the behavior of the objective function is analyzed. As well, the influence of the quantitative correlation between the swirling flow at the cone inlet and the analytical blade shape, flow rate, and swirl number using the best inlet velocity profiles is evaluated. We also include a discussion on the development of a flow structure caused by the inlet swirl parameters. Finally, we present an analysis of the influence of flow rate and swirl number on the behavior of the optimization process.