In a previous study, lead (Pb) and cadmium (Cd) have been removed successfully from aqueous solutions using naturally occurring saponin isolated from Olea europaea and Citrus aurantium leaves. It was shown that biochemical removal of heavy metals was affected greatly by setting time, the concentration of heavy metal, concentration of saponin extract, and pH value. The process can easily remove heavy metals biochemically via coordinated complex formations between a central heavy metal and saponin as a natural bio-ligand. Accordingly, the effect of chemical factors is well-known but, the effect of physical factors is not. Our present work is focuses on the effect of some physical operational variables on the performance of saponin extraction for the removal of heavy metals. Temperature, agitation, and the synergism between them were the main physical factors that influence the biochemical reaction under investigation. Also, density, moisture content, and organic/inorganic contents have been determined for Olea europaea and Citrus aurantium leaves.