Electrochemical hydrogen compressor (EHC) has proven to be a valid solution for the development of Fuel Cell Vehicles and hydrogen refueling stations. Hydrogen pressures up to 1000 bar can be reached by using an EHC. However, low compression efficiencies are obtained at very high pressures, mainly because of difficulties in sealing and hydrogen back diffusion through the polymer electrolyte membrane (PEM). Moreover, the performances of an EHC are affected by local dehydration of the PEM. A segmented cell of active area 30 x 1 cm2 and divided into 20 segments of 1.5 cm2 was used to investigate the local behavior of an EHC. Such a system allowed measuring the current density along the channel direction and the resistances of each single segment by impedance spectroscopy, making possible the evaluation of the local water transport through the PEM. In fact, heterogeneities in the distribution of the electric resistances were observed, reflecting the unbalanced contribution of the two water transport mechanisms along the PEM, i.e. electro-osmosis and water back diffusion. A pseudo 2D model, which simulates the mass and energy transfer occurring in the EHC, was developed along with the experimental investigation. It was observed that these heterogeneities can significantly alter the efficiency of an EHC. Hence, several parameters affecting the performance of an EHC, such as the humidity of the inlet flow, temperature, PEM thickness, discharge pressure and stoichiometric ratio, were investigated in order to optimize the system and enhance its overall efficiency.