Cellulose nanocrystals (CNCs) have shown promise for the development of multifunctional materials for many research communities, ranging from bioresource engineering and biomedical engineering to materials science and engineering. However, accessible hydroxyl (OH) groups on the surface of colloidal CNCs at the (11̅0)β/(100)α and (110)β/(010)α facets and the intermolecular hydrogen bonding (H-bonds) between these OH groups account for the instability of self-assembled CNC structures in moist environments, limiting their practical uses to dry media. In this work, accessible OH groups of CNCs were crosslinked using two crosslinkers, that is, glutaraldehyde (GA) and epichlorohydrin (EC), to form nanoparticle-based hydrogels with tunable physicochemical properties. The intensity of the intermolecular H-bonds was controlled by the type and concentration of crosslinkers as well as the CNC concentration. Rheological analyses through the loss tangent were used to determine the degree of crosslinking with maximal values beyond 90%. Fourier-transform infrared spectroscopy demonstrated that H-bond intensity was inversely proportional to the degree of crosslinking for both GA and EC, indicating a dissimilar crosslinking mechanism for GA and EC in acidic and alkaline pH conditions, respectively. Atomic force microscopy and wettability analyses showed a significant increase in the surface roughness from 3.2 ± 0.41 nm (pure CNC) to 31.5 ± 1.08 nm (CNCs crosslinked by GA) and 23.8 ± 0.14 nm (CNCs crosslinked by EC) and water contact angle from 13° (pure CNC) to 108° (CNCs crosslinked by GA) and 104° (CNCs crosslinked by EC). Moreover, optimum water absorption values were found at 157.67 ± 2.01 g and 173.59 ± 1.26 g of water for 1 g of freeze-dried hydrogels for 10% GA and 1% EC, respectively. The results aligned with reaction conditions that led to maximal degrees of crosslinking and indicated the transformation of surface chemistry from a hydrophilic to a hydrophobic network as well as tunable topology and aqueous stability of self-assembled structures made from crosslinked CNCs. This technology demonstrated the potential of crosslinked CNCs with tunable physicochemical properties for use as advanced building blocks to produce 2D and 3D structures for their related functions.