Access to efficient and affordable materials for water purification is of fundamental importance for the sustainable development of our society. Materials based on protein nanofibrils (PNFs) from agricultural waste- or side streams have recently been shown to have excellent adsorption properties for organic as well as inorganic pollutants. We here investigate the role of the nanostructure in aerogels made from whey protein isolate for the removal of a model pollutant (ibuprofen) from water. Water stable aerogels were produced using a recently developed approach for intrinsic crosslinking of protein materials without requiring additives. By comparing materials made from PNFs and from non-fibrillar whey protein we find that the fibrils have dual roles in enhancing the ibuprofen binding capacity. The PNFs do have a higher direct binding affinity but they also remodel the cell wall structures of the aerogels, resulting in a mesoporous network with enhanced ability of pollutant adsorption.