Purpose The goal of this study was to fabricate low-cost novel nanocomposite materials from agro-wastes of plant origin (modifiers), silver nanoparticles, and functionalized multiwalled carbon nanotubes (f-MWCNTs) with the potential to disinfect polluted aqueous systems. Methods Silver ions were first bio-reduced by the methanolic extract of Funtumia elastica husk onto the walls of acid-functionalized MWCNTs (f-MWCNTs), and the product obtained was modified by making use of Annona muricata petals (AMB), Funtumia elastica husk (FEB), or Acacia xanthophloea stem bark (AXB). Analytical techniques such as Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, powder X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), field-emission scanning electron microscopy (FE-SEM), and thermogravimetric analysis (TGA) were used to characterize the composites. Results The results showed the formation of homogenous composites with improved thermal stability and high surface area. The antibacterial potential of the fabricated materials were evaluated against two bacterial species, namely, gram-negative Escherichia coli (ATCC 35218) and gram-positive Staphylococcus aureus (ATCC 219213) in water. The three composite materials and the nanohybrid (Ag/f-MWCNTs) showed significantly promising activities against the bacterial strains (above of 99.4% kill) whilst the others (biomass) exhibited marginal activities. However, the inhibitory effects of these materials were observed to be influenced by their concentration and the pH of the water, but were less impacted by changes in temperature. Conclusion The results herein indicate the potential of harnessing these nanocomposites as antimicrobial agents for water disinfection if conditions are properly optimised. Graphic Abstract