An electrochemical method is described for the qualitative or semi-quantitative analysis of mass transfer rates in organically modified silicas obtained by the co-condensation route. It is based on the dispersion of these solid particles into carbon paste matrices and the application of the resulting modified electrodes in the preconcentration analysis of a target electroactive probe according to the sequence “accumulation at open circuit—voltammetric detection”. In conditions where the accumulation step is diffusion-controlled, the current sampled during the detection step constitutes an indirect measurement of the speed at which the probe is reaching the active centers in the porous hybrid structure. Hg(II) was used as the probe, which is likely to bind to mesoporous silica spheres functionalized with either amine or thiol groups. These materials were obtained by self-assembly co-condensation of tetraethoxysilane (TEOS) and aminopropyltriethoxysilane (APTES) or mercaptopropyltrimethoxysilane (MPTMS) precursors in various ratios, in the presence of a cationic surfactant acting as a template. Special attention was given to highlight the influence of the materials structure and the density of functional groups on the access rates to the binding sites. The reliability of the method was checked by comparing the results to those obtained from conventional batch experiments. Mass transfer rates were found to be optimum in mesoporous solids displaying short range structural order, which were obtained from an organosilane content of 20% in the starting sol.