Single molecule electron devices (SMEDs) have been widely studied through both experiments and theoretical calculations because they exhibit certain specific properties that general macromolecules do not possess. In actual SMED systems, a residual water molecule strongly affects the electronic properties of the SMED, even if only one water molecule is present. However, information about the effect of H2O molecules on the electronic properties of SMEDs is quite limited. In the present study, the effect of H2O on the ON-OFF switching property of benzene-based molecular devices was investigated by means of a direct ab initio molecular dynamics (AIMD) method. T- and H-shaped benzene dimers and trimers were examined as molecular devices. The present calculations showed that a H2O molecule accelerates the π-stacking formation in benzene molecular electronic systems. The times of stacking formation in a benzene dimer cation (n = 2) were calculated to be 460 fs (H2O) and 947 fs (no-H2O), while those in a trimer cation (n = 3) were 551 fs (H2O) and 1019 fs (no-H2O) as an average of the reaction time. This tendency was not dependent on the levels of theory used. Thus, H2O produced positive effects in benzene-based molecular electronics. The mechanism of π-stacking was discussed based on the theoretical results.