The coagulation or flocculation of cohesive clay suspensions is one of the most widely used treatment technologies for contaminated water. Flocculated clay can transport pollutants and nutrients in ground water. Coagulants are used to accelerate these mechanisms. However, existing coagulants (e.g., polyacrylamide, polyaluminum chloride) are known to have harmful effects in the environment and on human health. As an alternative, eco-friendly coagulant, this study suggests ε-polylysine, a cationic biopolymer fermented by Streptomyces. A series of sedimentation experiments for various ε-polylysine concentrations were performed, and the efficiency of sedimentation with ε-polylysine was estimated by microscopic observation and light absorbance measurements. Two types of sedimentation were observed in the experiments: accumulation sedimentation (at 0.15%, 0.20%, 0.25% ε-polylysine) and flocculation sedimentation (at 0%, 0.1%, 0.5%, 1.0%, 2.0% ε-polylysine). These sedimentation types occur as a result of the concentration of counter ions. Additionally, the performance of εpolylysine was compared with that of a previously used environmentally friendly coagulant, chitosan. The obtained results indicate that flocculation sedimentation is appropriate for contamination removal and that ε-polylysine functions more efficiently for clay removal than chitosan. From the experiments and analysis, this paper finds that polylysine is an alternative eco-friendly coagulant for removing chemical contaminants in groundwater.