Biosorption of Cu(II) onto coconut shell, an agricultural biomaterial, was studied in a fixed-bed column. The Cu(II) biosorption column had the best performance at 10 mg L−1 inlet Cu(II) concentration, 10 mL min−1 flow rate and 20 cm bed depth. The equilibrium uptake of Cu(II) amounted to 7.25 mg g−1. The simulation of the breakthrough curve was successful with the BDST and Yoon–Nelson models, but the entire breakthrough curve was best predicted by the Clark model. The design of a fixed bed column for Cu(II) removal from wastewater by biosorption onto coconut shell can be done based on these models.