The removal of Cu(II) ions from aqueous solutions at a pH of 5.0 was carried out using fixed-bed columns packed with alginate-chitosan (Alg-Ch) or alginate-chitosan sulfate (Alg-ChS) hydrogel beads. The effect of the initial Cu(II) concentration, flow rate, pH, and height of the column on the amount of Cu removed by the column at the breakpoint and at the exhaustion point is reported. The pH of the solution at the column’s exit was initially higher than that at the entrance, and then decreased slowly. This pH increase was attributed to proton transfer from the aqueous solution to the amino and COO− groups of the hydrogel. The effect of operating conditions on the mass transfer zone (MTZ) and the length of the unused bed (HLUB) is reported. At the lower flow rate and lower Cu(II) concentration used, the MTZ was completely developed and the column operated efficiently; by increasing column height, the MTZ has a better opportunity to develop fully. Experimental data were fitted to the fixed-bed Thomas model using a non-linear regression analysis and a good correspondence between experimental and Thomas model curves was observed.