The determination of the labile fraction and total concentration of copper and mercury in different sites of the Lagoon of Venice, using a remote electrochemical sensor based on a gold fiber microelectrode, is presented. The remote sensor was used in conjunction with either potentiometric stripping analysis (PSA) or square-wave anodic stripping voltammetry (SWASV). The results obtained show that using PSA, in situ detection of the labile fraction of both metals can be achieved down to 0.22 and 0.04 ppb for copper and mercury, respectively. Under these conditions the relative standard deviation (RSD) was within 8 and 10% for copper and mercury, respectively. In contrast, no reliable in situ data could be obtained with SWASV. This is attributed to the lack of suitable software for baseline treatment with this technique. Laboratory measurements were employed for total concentration determination of the metal ions. The total concentration was obtained after acidification of the sample to pH 1 with HCl. Under these conditions, the concentration of both copper and mercury increased by about one order of magnitude. This allowed the determination of the two ions by SWASV, whereas the overlap of the stripping peaks of copper and mercury prevented their determination by PSA. The precision for the total concentration was also satisfactory, the RSD being 5 and 7% for copper and mercury, respectively. The effect of the matrix on the PSA and SWASV responses is discussed. Total concentrations determined by the anodic stripping technique are compared with those found by atomic absorption spectrometry.