Cellulose nanocrystals (CNCs) have drawn considerable attention for their use in optical and sensor applications due to their appealing properties of chiral nematic photonic structures. However, the flexibility and water instability of neat CNC chiral nematic films are questionable and compromise their outstanding properties. We propose a room-temperature process for fabricating flexible, water-stable chiral nematic CNC films. Aqueous glutaraldehyde (GA) was first mixed with CNCs, and then free-standing films were formed by evaporation-induced self-assembly. The chiral nematic dry films that formed were then exposed to hydrochloric acid vapor for subsequent GA cross-linking with CNCs. The GA cross-linked CNC films had a highly ordered chiral nematic organization. The enhanced water stability of the films was demonstrated by using GA cross-linked CNC films as freestanding template substrates for conducting polymers (polypyrrole) and metal oxides (iron oxide) to form flexible chiral nematic photonic hybrids.