Effective and efficient removal of both heavy metal pollutants and bacterial contamination from fresh water is an open issue, especially in developing countries. In this work, a novel eco-friendly functional composite for water treatment application was investigated. The composite consisted of electrospun nanofiber membrane from blended polyvinyl alcohol (PVA)/iota carrageenan (IC) polymers doped with equal concentrations of graphene oxide (GO) nanoparticles and polyaniline (PANI). The effectiveness of this composite as a water purification fixed-bed filter was optimized in a batch system for the removal of cadmium (Cd+2) and lead (Pb+2) ions, and additionally characterized for its antimicrobial and antifungal properties and cytotoxicity effect. The fiber nanocomposite exhibited efficient antibacterial activity, with maximum adsorption capacity of about 459 mg g−1 after 120 min for Cd+2 and of about 486 mg g−1 after 90 min for Pb+2. The optimized conditions for removal of both metals were assessed by using a response surface methodology model. The resulting scores at 25 °C were 91.4% (Cd+2) removal at 117 min contact time for 89.5 mg L−1 of initial concentration and 29.6 cm2 membrane area, and 97.19% (Pb+2) removal at contact time 105 min for 83.2 mg L−1 of initial concentration and 30.9 cm2 nanofiber composite membrane. Adsorption kinetics and isotherm followed a pseudo-second-order model and Langmuir and Freundlich isotherm model, respectively. The prepared membrane appears to be promising for possible use in domestic water purification systems.