The present study aimed to develop and optimize a method to obtain cellulose nanocrystals from the agricultural by-products rice husk and straw and to evaluate their electrostructural modifications in the presence of metallic ions. First, different particle formation conditions and routes were tested and analyzed by spectrophotometry, dynamic light scattering (DLS), and Zeta potential measurements. Then, electrostructural effects of ions Na(I), Cd(II), and Al(III) on the optimized nanoparticles were analyzed by atomic force microscopy (AFM), scanning electron microscopy (SEM), and electrical conductivity (EC) assessments. The produced cellulose nanocrystals adopted a rod-like shape. AFM height distribution and EC data indicated that the nanocrystals have more affinity in binding with Na(I) > Al(III) > Cd(II). These data suggest that the use of these cellulose nanocrystals in the bioremediation field is promising, both in metal sorption from wastewater and as an alternative for water desalination.