Graphene-based 3D macroscopic aerogels with their hierarchical porous structures and mechanical strength have been widely explored for removing contaminants from water. However, their large-scale manufacturing and application in various water treatment processes are limited by their scalability. In this study, we report a proof-of-concept direct ink writing (DIW) 3D printing technique and subsequent freeze-drying to prepare graphene-biopolymer aerogels for water treatment. To provide appropriate rheology for DIW printability, two bio-inspired polymers, polydopamine (PDA) and bovine serum albumin (BSA), were added to the graphene-based ink. The biopolymers also contributed to the contaminant removal capacity of the resultant graphene-polydopamine-bovine serum albumin (G-PDA-BSA) aerogel. The physicochemical properties of the aerogel were thoroughly characterized from the nano- to macroscale. The 3D printed aerogel exhibited excellent water contaminant removal performance for heavy metals (Cr(VI), Pb(II)), organic dyes (cationic methylene blue and anionic Evans blue), and organic solvents (n-hexane, n-heptane, and toluene) in batch adsorption studies. The electrostatic interaction dominated the removal of heavy metals and dyes while the hydrophobic interaction dominated the removal of organic solvents from water. Moreover, the aerogel showed superb regeneration and reuse potential. The aerogel removed 100% organic solvents over 10 cycles of regeneration and reuse; additionally, the removal efficiencies for methylene blue decreased by 2–20% after the third cycle. The fit-for-design 3D printed aerogel was also effectively used as a bottle-cap flow-through filter for dye removal. The potential and vision of the 3D printing approach for graphene-based water treatment presented here can be extended to other functional nanomaterials, can enable shape-specific applications of fit-for-purpose adsorbents/reactors and point-of-use filters, and can materialize the large-scale manufacturing of nano-enabled water treatment devices and technologies.