In this paper, the surface impedance influence on scattering matrix of antenna array of identical semi-infinite plane waveguides with a common flange is investigated. Impedance flange model takes into account the imperfect flange material conductivity and flange surface structure (gratings, grooves, etc). A method of scattering matrix elements computation based on a system of linear equations is proposed. Results of numerical investigation for antenna array of six waveguides are presented. It is demonstrated that for antenna array with capacitive type of flange impedance, mutual coupling between elements is less than for the perfectly conductive flange case. Values of reflection coefficients increase on the high frequencies, in particular, on the upper bound of single-mode band they increase almost fourfold and achieve up to 4% of power. For antenna array with inductive type of flange impedance the values of reflection coefficients are greater than values of the perfectly conductive case on the full single-mode frequency band. Transmission coefficients amplitudes do not decrease when the frequency increases. It is caused by influence of a surface wave. This fact must be taking into account in the process of wideband phased waveguide array development.