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In order to improve water and oxygen barrier properties, the surface of two commercial medical grade polyurethane (PU) membranes (Chronoflex® AR-LT and Bionate® II) was modified by a spray deposited film of poly(ethylene-co-vinyl alcohol) (EVOH). The influence of the temperature, the deposited layer thickness and the EVOH ethylene group percentage (27%, 32%, and 44% for EVOH27, EVOH32, and EVOH44, respectively) on the barrier properties of the PU/EVOH multilayered membranes was investigated. The increase of the EVOH layer thickness leads to higher oxygen barrier properties (the highest barrier improvement factor of 412 was obtained). However, in case of the deposited layer thickness higher than 18 μm, microcracks appeared on the treated surface promote a significant loss of the barrier effect. Due to its higher crystallinity degree, EVOH27 provides a higher oxygen barrier effect compared to EVOH32 and EVOH44. On the contrary, an increase of the water barrier properties was observed with the increase of the percentage of ethylene groups. Moreover, the delamination of the EVOH layer was noted after water permeation, especially in case of EVOH44, which is the most hydrophobic layer. Nevertheless, significant decrease of the water and oxygen permeability of the modified PU membranes was achieved, thus showing the benefit of using the EVOH spray deposition for the biomedical application, which requires high performance material with flexible and barrier properties.