The structural properties and aggregation behavior of carboxymethylated cellulose nanocrystals (CNC-COOH) were analyzed with small angle neutron scattering (SANS), transmission electron microscopy (TEM), atomic force microscopy (AFM), and dynamic light scattering (DLS) and compared to sulfuric acid hydrolyzed cellulose nanocrystals (CNC-SO3H). The CNC-COOH system, prepared from single carboxymethylated cellulose nanofibrils, was shown to laterally aggregate into 2D-stacks that were stable both in bulk solution and when adsorbed to surfaces. CNC-SO3H also showed a 2D aggregate structure with similar cross sectional dimensions (a width to height ratio of 8) as CNC-COOH, but a factor of 2 shorter length. SANS and DLS revealed a reversible ordering of the 2D aggregates under semidilute conditions, and a structure peak was observed for both systems. This indicates an early stage of liquid crystalline arrangement of the crystal aggregates, at concentrations below those assessed using birefringence or polarized optical microscopy.