Environmental risks can arise from the existence of heavy metals in wastewater and their land disposal. To address this concern, a mathematical technique is introduced in this article that enables the anticipation of breakthrough curves and the imitation of copper and nickel ion separation onto nanocellulose in a fixed-bed system. The mathematical model is based on mass balances for copper and nickel and partial differential equations for pore diffusion in a fixed bed. The study evaluates the impact of experimental parameters such as bed height and initial concentration on the shape of the breakthrough curves. At 20 °C, the maximum adsorption capacities for copper and nickel ions on nanocellulose were 5.7 mg/g and 5 mg/g, respectively. The breakthrough point decreased with increasing solution concentration at higher bed heights, while at an initial concentration of 20 mg/L, the breakthrough point increased with bed height. The fixed-bed pore diffusion model showed excellent agreement with the experimental data. The use of this mathematical approach can help alleviate the environmental hazards that arise from the presence of heavy metals in wastewater. The study highlights the potential of nanocellulose as a material for membrane technology, which can effectively address these risks.