Cyanotoxins such as microcystin-LR (MC-LR) represent a global environmental threat to ecosystems and drinking water supplies. The study investigated the direct use of graphene as a rational interface for removal of MC-LR via interactions with the aromatic ring of the ADDA1 chain of MC-LR and the sp2 hybridized carbon network of graphene. Intra-particle diffusion model fit indicated the high mesoporosity of graphene provided significant enhancements to both adsorption capacities and kinetics when benchmarked against microporous granular activated carbon (GAC). Graphene showed superior MC-LR adsorption capacity of 75.4 mg/g (Freundlich model) compared to 0.982 mg/g (Langmuir model) for GAC. Sorption kinetic studies showed graphene adsorbs 99% of MC-LR in 30 min, compared to zero removal for GAC after 24 hr using the same MC-LR concentration. Density functional theory (DFT), calculations showed that postulated π-based interactions align well with the NMR-based experimental work used to probe primary interactions between graphene and MC-LR adduct. This study proved that π-interactions between the aromatic ring on MC-LR and graphene sp2 orbitals are a dominant interaction. With rapid kinetics and adsorption capacities much higher than GAC, it is anticipated that graphene will offer a novel molecular approach for removal of toxins and emerging contaminants with aromatic systems.