In this study, a copolymer of aniline and indole P(ANI-co-IN) and its nanocomposites based on graphene oxide (GO) and functional carbon nanotubes (CNT-COOH) were synthesized by heterogeneous emulsion polymerization. The prepared adsorbents were evaluated for the removal of cationic dyes, methylene blue (MB) and malachite green (MG), from aqueous solution. The physical properties of the novel copolymer and nanocomposite adsorbent were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy and thermogravimetric analysis (TGA). The isotherms and kinetics of the adsorption of MB and MG onto nanoadsorbents have been studied under various experimental parameters such as initial dye concentration, contact time, solution pH and adsorbent dosage. Batch adsorption results fitted well with the Langmuir model for both P(ANI-co-IN)/CNT-COOH and P(ANI-co-IN)/GO nanoadsorbents based on correlation values (R2) of 0.9973 and 0.9970, respectively. The maximum adsorption capacity of the nanocomposites for MB and MG was 384 and 434 mg g−1, respectively. The kinetics of the adsorption process was found to follow a pseudo-second-order kinetics for both nanocomposites indicating chemical sorption as the rate determining step. The synthesized nanoadsorbents revealed improvements in terms of adsorption capacity for the dyes as a result of their high surface area and large amount of interactive functional groups. Among the nanocomposites, P(ANI-co-IN)/CNT-COOH showed much higher antibacterial activity toward Gram-negative bacteria Escherichia coli (E. coli).