Polymerization of citric acid onto the surface of oxidized multiwall carbon nanotubes led to MWCNT-graft-poly(citric acid) (MWCNT-g-PCA) hybrid materials. Because of the presence of conjugated citric acid branches, synthesized MWCNT-g-PCA hybrid materials were not only soluble in water but also able to trap water-soluble chemical species and metal ions. Trapping of pesticides such as zineb and mancozeb in aqueous solution by MWCNT-g-PCA hybrid materials led to encapsulated pesticide (EP) in the polycitric acid shell. Optimum conditions for encapsulation of zineb and mancozeb in hyperbranched polycitric acid such as pH, time of stirring, and temperature were investigated by the UV-vis spectroscopy method. Encapsulation of pesticides on CNT-g-PCA hybrid material was confirmed via TEM analysis. Experiments indicated that new the CNT-g-PCA-EP hybrid material in comparison with bulk pesticide had a superior toxic influence on Alternaria alternata fungi.