Metal nanostructures are promising novel labels for microarray-based biomolecular detection. Additional silver deposition on the surface-bound labels strongly enhances the sensitivity of the system and can lead to continuous metal areas, which enable an electrical readout especially for simple and robust point-of-care analyses. In this paper, atomic force microscopy (AFM) was used to study different routes of metal deposition on labelled DNA-DNA duplexes in electrode gaps. Besides the well-established metal-induced silver enhancement, a recently introduced enzymatic silver deposition was applied and proved highly specific. The in situ characterization was especially focused on the nanostructure percolation-the moment at which the nanoparticulate film becomes continuous and electrically conducting. The formation of conducting paths, continuous from one electrode to the other, was followed by complementary electrical measurements. Thereby, a percolation threshold was determined for the surface coverage with metal structures, i.e. the required metallized area to achieve conductance. Complementary graphic simulations of the growth process and graphic 'conductance measurements' were developed and proved suitable to model the metal deposition and electrical detection. This may help to design electrode arrays and identify optimum enhancement parameters (required seed concentration and shell growth) as well as draw quantitative conclusions on the existing label (i.e. analyte) concentration.