Fully biobased composite membranes for water purification were fabricated with cellulose nanocrystals (CNCs) as functional entities in chitosan matrix via freeze-drying process followed by compacting. The chitosan (10 wt%) bound the CNCs in a stable and nanoporous membrane structure with thickness of 250–270 μm, which was further stabilized by cross-linking with gluteraldehyde vapors. Scanning electron microscopy (SEM) studies revealed well-individualized CNCs embedded in a matrix of chitosan. Brunauer, Emmett and Teller (BET) measurements showed that the membranes were nanoporous with pores in the range of 13–10 nm. In spite of the low water flux (64 L m⁻² h⁻¹), the membranes successfully removed 98%, 84% and 70% respectively of positively charged dyes like Victoria Blue 2B, Methyl Violet 2B and Rhodamine 6G, after a contact time of 24 h. The removal of dyes was expected to be driven by the electrostatic attraction between negatively charged CNCs and the positively charged dyes.