The self-assembly of nanocellulose and graphene oxide into highly porous biohybrid materials has inspired the design and synthesis of multifunctional membranes for removing water pollutants. The mechanisms of self-assembly, metal ion capture, and cluster formation on the biohybrids at the nano- and molecular scales are quite complex. Their elucidation requires evidence from the synergistic combination of experimental data and computational models. The AFM-based microscopy studies of (2,2,6,6-tetramethylpiperidine-l-oxylradical)-mediated oxidized cellulose nanofibers (TOCNFs), graphene oxide (GO), and their biohybrid membranes provide strong, direct evidence of self-assembly; small GO nanoparticles first attach and accumulate along a single TOCNF fiber, while the long, flexible TOCNF filaments wrap around the flat, wide GO planes, thus forming an amorphous and porous biohybrid network. The layered structure of the TOCNFs and GO membrane, derived from the self-assembly and its surface properties before and after the adsorption of Cu(II), is investigated by advanced microscopy techniques and is further clarified by the ReaxFF molecular dynamics (MD) simulations. The dynamics of the Cu(II)-ion capture by the TOCNF and GO membranes in solution and the ion cluster formation during drying are confirmed by the MD simulations. The results of this multidisciplinary investigation move the research one step forward by disclosing specific aspects of the self-assembly behavior of biospecies and suggesting effective design strategies to control the pore size and robust materials for industrial applications.