To prevent eutrophication, controlling the phosphate concentration levels is one of the most important issues in surface water management. One of the most utilized methods is phosphate adsorption. However, its application faces a bottleneck due to the unclear understanding of adsorption and interaction mechanisms. The present work unlocks the phosphorus adsorption mechanisms in three-dimensional reduced graphene oxide with different reduction levels and pore sizes to remove phosphate from water using experiments and multiscale simulations. Experiments were performed to evaluate the influence of pH, ionic strength, and temperature on the adsorption. Molecular Dynamics and Ab Initio simulations evaluated the influence of the pore size and oxidation degrees of the materials. We show that the adsorption capacity of the materials increases with increasing pH and ionic strength and decreasing temperature. It is observed that the more oxidized the material and the less compact the structure, the better the adsorption. These results are theoretically explained in terms of the interaction of functional groups and the clustering of phosphate ions, which results in better adsorption in materials with larger pores. The underlying mechanisms for the 3D-reduced graphene oxide performance were confirmed by spectroscopy analysis. All the results show that 3D-reduced graphene oxide can sorb phosphate in different complex water remediation systems with characteristics that can be modulated by changing the material synthesis method.