Multiwalled carbon nanotubes (MWCNTs) were used as the active elements for the first time for affinity-based elimination of ionic dyes. MWCNTs were encapsulated in cross-linked alginate (ALG) microvesicles using Ba2+ as the bridging ion. The Ba2+-alginate matrix constitutes a cage which holds the physically trapped MWCNTs. The cage carries negative charges on its surface. The cage restricts the access of anions of large molecular weight, such as humic acids, because of electrostatic repulsion. The cage also restricts the access of colloids of large size, because of size exclusion. Ionic dyes partition into the cage and then are captured by MWCNTs probably on the basis of van der Waals interactions occurring between the hexagonally arrayed carbon atoms in the graphite sheet of MWCNTs and the aromatic backbones of the dyes. As a result of these interactions the target species, namely, the ionic dyes, are eliminated efficiently by the MWCNTs of Ba2+-ALG/MWCNT composite adsorbents. The adsorptive capacities for elimination of acridine orange, ethidium bromide, eosin bluish, and orange G (the model species used for this study) were found as high as 0.44, 0.43, 0.33, and 0.31 micromol, respectively, for 1.0 mg of the caged MWCNTs. Adsorptive experiments with carbon nanofibers and activated carbons as the adsorbents were also performed. The MWCNT-based adsorbents provided the best capability for the affinity-based elimination of these targeted species. Biocompatibility experiments performed in vitro and in vivo provided promising results, suggesting potential applications of the caged MWCNTs in in situ environmental remediation.