A fuel cell based system's performance is mainly identified in the overall efficiency, strongly depending on the amount of power losses due to auxiliary devices to supply. In such a situation, everything that causes either a decrease of the available power output or an increment of auxiliary losses would determine a sensible overall efficiency reduction. This situation inevitably pops up in case of water flooding, a phenomenon that causes a reduction of the number of chemical reactions between reactants (O2 and H2) that can take place at the reaction sites, as liquid water would obstruct the catalyst and gas diffusion layers pores the gases have to flow through, while at the same time determining a higher pressure drop of the flow passing along the channels, as the liquid water will have to be blown away: the two main effects are a drop in the production of electricity with respect to its theoretical amount (corresponding to the stoichiometric reaction) and an increment of the pump electric load required to overcome the overall pressure drop across the cell. A suitable solution has been identified in designing the fuel cell bipolar plate's channels in such a manner to allow an optimal water management at a desired fuel cell design point (depending on the mission requirements). In order to do that, the approach the research team has experienced consists in simulating the PEM fuel cell through the use of a proprietary model, based on the co-operation of a CFD solver (CD-adapco STAR-CCM+) and a numeric computation software (Mathworks Matlab), able to estimate the baseline cell's performance. Starting from this point, in order to overcome the impossibility of carrying out a suitable bi-phase simulation in STAR-CCM+ (version 5.06), a dedicated analytical model evaluates the amount of liquid water produced by the cell, this data being a fundamental input to be used to address the performance reduction due to the presence of the liquid water itself. Through the use of a mesh morphing technique applied directly on the plate's channels, from the baseline geometry a new channels shape will be configured: the objective is to counteract the effect of an increment of the pressure drop along the flow path, thus not impacting on the reactants pump workload, i.e. preserving the overall system's efficiency by containing the auxiliary losses. The baseline bipolar plate configuration and the modified one have then been tested separately and the results have been compared, showing a valuable impact of the morphing technique on the overall cell performance: a reduction in the overall pressure drop has been identified, this being the main result the researchers have been working for, as well as a better membrane electrical conductivity (due to a satisfactory membrane humidification). By the way, a CAE centric approach has been adopted to give to the user a flexible and powerful means to design an optimal geometry, while respecting the physical constraints.