Bio-based eco-friendly cellulose nanocrystals (CNCs) gain an increasing interest for diverse applications. We report the results of an investigation of hydrogels spontaneously formed by the self-assembly of carboxylated CNCs in the presence of CaCl2 using several complementary techniques: rheometry, isothermal titration calorimetry, FTIR-spectroscopy, cryo-electron microscopy, cryo-electron tomography, and polarized optical microscopy. Increasing CaCl2 concentration was shown to induce a strong increase in the storage modulus of CNC hydrogels accompanied by the growth of CNC aggregates included in the network. Comparison of the rheological data at the same ionic strength provided by NaCl and CaCl2 shows much higher dynamic moduli in the presence of CaCl2, which implies that calcium cations not only screen the repulsion between similarly charged nanocrystals favoring their self-assembly, but also crosslink the polyanionic nanocrystals. Crosslinking is endothermic and driven by increasing entropy, which is most likely due to the release of water molecules surrounding the interacting COO− and Ca2+ ions. The hydrogels can be easily destroyed by increasing the shear rate because of the alignment of rodlike nanocrystals along the direction of flow and then quickly recover up to 90% of their viscosity in 15 s, when the shear rate is decreased.