Boats are an important mean of transport, for passengers and cargo, mainly in countries with high water wealth. Nowadays, electrification of transport includes water alternatives, but the efficient use of energy is still a key issue. Energy consumption in electrically powered boats is highly influenced by several technical domains (e.g., hydrodynamics, battery, and propulsion). As literature reports advances in some of those domains, this article focuses on the "propulsion system (PS)" (motor–transmission–propeller) design and optimization. When implementing an electric motor, the interaction of mechanical components may be analyzed to find the optimal variables that will define the boat performance and the optimal motor–transmission–propeller combination. This article presents a methodology for multivariable optimization to maximize the overall efficiency of the PS, and therefore autonomy, in electric boats design. It proposes an approach from the physical variables that define the performance of the PS's components, through an optimality problem formulation and an exhaustive search model that considers all possible values of the key design parameters. A case study is presented for an electrically powered riverboat, where the proposed methodology enabled an improvement between 4% and 5% in the overall efficiency of the PS. This allows better use of the limited available energy with a gain of 2.9 km (7%) in the most favorable case.