In this paper, the transport of Cu(II) in the presence of lipophilic Cu(II) organic complexes through permeation liquid membranes (PLMs) have been investigated. In natural waters, small organic compounds, which form liposoluble neutral complexes with Cu(II), are potentially toxic and bioavailable. Hence, to understand the role of liposoluble Cu(II) complexes in natural waters, four organic ligands: phthalic acid, bipyridyl, pyrocatechol and hydroxyquinoline, which form uncharged or lipophilic Cu(II) complexes, were tested. The results showed that the transport of lipophilic Cu(II) complexes through PLM depends on the lipophilicity of the complex. Applications of PLMs in natural waters are presented.