Chitosan-based hybrid nanocomposites, containing cellulose nanocrystals (CNCs), graphene oxide (GO), and borate as crosslinking agents, were successfully prepared by solution-casting technique. The synergistic effect of the two fillers, and the role of the cross-linker, in enhancing the structural and functional properties of the chitosan polymer, was investigated. XPS results confirm the chemical interaction between borate ions and hydroxyl groups of chitosan, GO, and CNCs. The morphological characterization shows that the GO sheets are oriented along the casting surface, whereas the CNC particles are homogenously distributed in the sample. Results of tensile tests reveal that the presence of graphene oxide enhances the elastic modulus, tensile strength, elongation at break, and toughness of chitosan, while cellulose and borate induce an increase in the elastic modulus and stress at the yield point. In particular, the borate-crosslinked chitosan-based sample containing 0.5 wt% of GO and 0.5 wt% of CNCs shows an elongation at a break value of 30.2% and a toughness value of 988 J*m−3 which are improved by 124% and 216%, respectively, compared with the pristine chitosan. Moreover, the water permeability results show that the presence of graphene oxide slightly increases the water barrier properties, whereas the borate and cellulose nanocrystals significantly reduce the water vapor permeability of the polymer by about 50%. Thus, by modulating the content of the two reinforcing fillers, it is possible to obtain chitosan-based nanocomposites with enhanced mechanical and water barrier properties which can be potentially used in various applications such as food and electronic packaging.