We reported a series of tough nanocomposite hydrogels with good antifouling properties based on quaternized hybranched polyethylenimine (HPEI) nanoparticles. The quaternized HPEI nanoparticles acted as both cross-linkers to produce tough hydrogels and antibacterial agents to prevent fouling attachments. Compared with the polymer hydrogel, these nanocomposite hydrogels exhibited significantly improved mechanical properties. The mechanical strength of the nanocomposite hydrogels had a strong dependence with proportion of the quaternized HPEI nanoparticles. Furthermore, the anti-algae/bacterial assay indicated the nanocomposite hydrogels showed better antimicrobial and anti-algae performances due to the broad spectrum antimicrobial activity of Quaternary Ammonium Salts (QAS) functional groups.