In the search for a technically efficient and abundant adsorbent in water treatment processes, a bio-composite adsorbent derived from agricultural wastes has been identified as a potential candidate. In this study, eggshells and sugarcane bagasse were combined in varied proportions (1:0, 1:3, 1:1, 3:1 and 0:1) and applied as biosorbents in a lab-scale adsorption column. The effect of bed depth (4–12 cm) of the biosorbents was investigated which enabled the prediction of breakthrough curves for the removal of Pb (II) ions. The life span of the column was extended by increasing the bed depth of the column. The binary adsorbent of 1:3 weight ratio of <75 µm particle size showcased the highest removal efficiency of 91% at a bed depth of 12 cm. The mass transfer zone (MTZ) increased with increasing bed depth with a minor portion of the bed left unused, signifying that the process was highly efficient. The Thomas model constant, KTh, decreased with increasing bed depth with the maximum amount of Pb adsorbed being 28.27 mg/g. With the Yoon–Nelson model, KYN decreased with an increase in τ as the bed height increased. In this study, a novel approach was adopted where the proposed methodology enabled the use of a bio-composite adsorbent in heavy metal removal. The findings of this research will aid in the design and optimisation of the pilot-scale operation of environmentally friendly treatment options for metal laden effluent.