Fundamental studies involving divalent ion intercalated graphene-based hydrogel are still lacking in terms of their adsorption behavior towards dye pollutants. In this study, we prepared a self-assembled Mg2+ and Ca2+ intercalated reduced graphene hydrogel (rGH) using hydrothermal treatment to evaluate the intercalation impact on the adsorption capability towards cationic dyes, methylene blue and rhodamine B. The morphological, structural, thermal, and textural properties of the divalent ion intercalated reduced graphene hydrogels were studied using Fourier transform infrared spectrometer, thermogravimetric analysis, Raman spectroscopy, scanning electron microscope-energy dispersive spectroscopy, X-ray photoelectron spectroscopy, Brunauer–Emmett–Teller surface area analysis, and X-ray diffraction. The increased adsorption capacity of the divalent ion intercalated reduced graphene-based hydrogels towards the dye molecules resulted from the increase in the specific surface area and pore volume due to the Mg2+ and Ca2+ bridging that formed spaces between the graphene sheets framework. Adsorption kinetics and the equilibrium adsorption isotherm were fitted by a pseudo-second-order alongside intraparticle diffusion kinetic models and Langmuir isotherm respectively. In addition, the divalent ion intercalated reduced graphene hydrogel showed good generation after three cycles of simultaneous adsorption.