A complexing gel integrated microelectrode (CGIME) for direct measurements of free metal ion concentrations in natural waters has been developed. It is prepared by the successive deposition of microlayers of a chelating resin, an antifouling agarose gel and Hg on a 100-interconnected Ir-based microelectrode array. The trace metals of interest are in a first step accumulated on the chelating resin in proportion to their free ion concentration in solution, then released in acidic solution and detected simultaneously by using square wave anodic stripping voltammetry (SWASV). The reliability of this sensor for the simultaneous measurement of copper, lead and cadmium has been studied by a series of replicate laboratory tests. The proportionality between the voltammetric peak current intensity and the free metal ion concentrations in solution has been demonstrated by using malonate as a model ligand. Finally, the CGIME sensor was applied to the Cu and Pb free concentration measurement in sea water samples and the results compared to the free metal ion concentrations measured using hollow fiber based permeation liquid membrane (HF-PLM) coupled to inductively coupled plasma mass spectrophotometer (ICP-MS). Comparable concentration values were found for both metals with both techniques allowing to validate the CGIME measurements in complex media. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA.