3D porous graphene microarchitectures with aligned and continuous channels are of paramount interest for several applications such as pollutant removal, energy storage, or biomedical engineering. For these applications, an accurate control over the pore microstructure is of capital importance. Freeze casting is a well-stablished technique to prepare graphene aerogels with unidirectional channels. This technique is typically applied to plain GO colloids, leading to discontinuous microchannels. Herein we have carried out the freeze process starting directly with partially reduced graphene (rGO) hydrogels prepared by a prior hydrothermal treatment in autoclave. This approach leads to the formation of aerogels with aligned and continuous microchannels, enabled by an intermediate cross-linking degree of the rGO nanosheets, carefully controlled by keeping the time of the prior hydrothermal process between the thresholds of 45–75 min. To the best of our knowledge, the effect of the degree of cross-linking in the freeze casting process is not yet reported. The resulting rGO aerogels with highly aligned microchannel structure reveal superior properties over its isotropic counterpart of randomly oriented pores for the absorption of nonpolar solvents and the selective adsorption of an aromatic compound dissolved in an alkane. Our combined hydrothermal freeze casting approach thus affords aligned microchannel rGO aerogels of enormous potential for environmental remediation.