The influence of 200 keV Ar-ion irradiation on the interlayer coupling in the Fe/Cr multilayer system exhibiting the giant magnetoresistance effect (GMR) is studied by conversion electron Mössbauer spectroscopy (CEMS), VSM hysteresis loops, magnetoresistivity and electric resistivity measurements and supplemented by the small-angle X-ray diffraction (SAXRD). The increase of Ar ion dose causes an increase of interface roughness, as evidenced by the increase of the Fe step-sites detected by CEMS as a result of which the GMR gradually decreases and vanishes at doses exceeding 1×1014 Ar/cm2. A degradation of GMR with increasing Ar-ion dose is related to the formation of pinholes between Fe layers and the decrease of the antiferromagnetically coupled fraction.