Ba2+-alginate coated vesicles (Ba2+-ALG) containing highly dispersed carbon nanofibers (CNFs) were successfully produced for the first time using an encapsulation technique. These Ba2+-ALG/CNFs composite vesicles showed high capabilities in trapping DNA-interactive types of chemicals. For example, 10.0 mL of the vesicles took 0.43 μmol of ethidium ions up from contaminated water within 8 min. Biocompatibility experiments performed in vitro and in vivo provided promising results, suggesting potential applications in in-situ environmental remediation. Kilogram quantities of the Ba2+-ALG/CNFs composite vesicles can be produced within a few hours.