The influence of ion implantation on the structure and properties of polymers is a very complex issue. Many physical and chemical processes taking place during ion bombardment must be taken into consideration. The complexity of the process may exert both positive and negative influence on the structure of the material. The goal of this paper is to investigate the influence of H+, He+ and Ar+ ion implantation on the properties of polypropylene membranes used in filtration processes and in consequence on fouling phenomena. It has appeared that the ion bombardment caused the chemical modification of membranes which has led to decrease of hydrophobicity. The increase of protein adsorption on membrane surface has also been observed.