The adsorption behaviors of methylene blue, rhodamine B, and methyl orange over graphene oxide were studied both experimentally and theoretically. From the experimental results and characterizations of fresh graphene oxide and graphene oxide after adsorption, selective adsorption of positive dye occurred via electrostatic interactions between the =N+H group (positive dipole from dye molecules, MB) and oxygen functional group of GO (negative dipole), as identified in the zeta potential, FT-IR, and XPS analyses. The selectivity for positive dye was rapid and quantitative where removal efficiencies of 97% and 88% were obtained for the positive dyes methylene blue and rhodamine B, respectively, within 15 min; the negative dye, methyl orange, was not adsorbed. The most probable arrangement of dyes on graphene oxide was evaluated using Ab initio molecular dynamics, and the adsorption energy was calculated. The most favorable adsorption configuration was found at 2298 fs for methyl orange and 2290 fs for methylene blue. Our results demonstrate that methylene blue is more strongly (- 2.25 eV/molecule) adsorbed on the GO surface than methyl orange (-1.45 eV/molecule).