The treatment of fish pond wastewater utilizing nanocomposites by batch adsorption using purified carbon nanotubes and silver-doped carbon nanotubes (CNTs) as nano-adsorbents was explored in this study. Ultraviolet spectroscopy, X-ray diffraction (XRD), and high-resolution transmission electron microscopy (HRTEM) were used to confirm the biosynthesized AgNPs. The metallic silver is associated with the peaks in the XRD pattern, and HRTEM studies indicated that AgNPs are between particle sizes of 11.12 and 15.39 nm. Purified carbon nanotubes (P-CNTs) and silver-doped carbon nanotubes (Ag-CNTs) were produced using a Fe–Ni/kaolin catalyst in a catalytic chemical vapour deposition process, followed by acid purification and doped with silver nanoparticles, respectively. HRTEM, HRSEM, FTIR, and BET were used to characterize the as-synthesized CNTs, P-CNTs, and Ag-CNTs. Both unpurified and purified CNTs were tube-like, extremely porous, and crystalline, with Ag-CNTs having a higher surface area (1068 m2/g) greater than P-CNTs (268.40 m2/g). The batch adsorption process was used to investigate the adsorption behaviour of P-CNTs and Ag-CNTs to remove Fe, Mn, and Zn from fish pond effluent as a function of contact time, adsorbent dosage, and temperature. The Freundlich isotherm described equilibrium sorption data better than the Langmuir isotherm, and the adsorption kinetics fit well with the pseudo-second-order model. A thermodynamic study of the adsorption process found that the change in Gibbs free energy was negative, indicating that the adsorption process was feasible and spontaneous. Consequently, it has been demonstrated that removing heavy metals from aquatic effluent using Ag-doped CNTs is effective in aquaculture.