A model is proposed to account for the influence of electrode surface modifications in electrochemical DNA sensors operating under flow conditions. With blocking self-assembled monolayers of double-stranded DNA, the performance of the electrochemical transduction signal in the presence of a redox mediator is generally attributed to the rate of long-range electron transfer or to the screening effects of the monolayers due to negatively charged DNA. The originality of this model is here to only consider the influence of non-linear mass transport at the free-remaining sites. The model was tested for the detection of microRNAs (21 nucleotides) by implementing microchannel electrodes in the presence of an equimolar mixture of Fe(CN)₆^3-/Fe(CN)₆^4-. Two operating conditions leading to distinct monolayer structures were investigated using Pt and Au electrodes. The model successfully simulated the voltammograms confirming the apparent decrease in the signal transduction kinetics due to altered mass transport. These results were supported by measurements in electrochemical impedance spectroscopy.