Bacterial contamination of water presents a serious public-health risk and creates a need for effective and affordable treatment methods. This study evaluated the antibacterial effectiveness of moringa, pawpaw and orange seed powders, green-synthesized magnesium oxide nanoparticles (MgONPs), and their combinations in experimentally contaminated water. Antibacterial performance was assessed using total viable count (TVC), total coliform count (TCC), bacterial occurrence, inhibition zones, minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The untreated contaminated water recorded TVC and TCC values of 257.33 ± 3.21 and 120.33 ± 4.04 CFU/mL, respectively, and contained Escherichia coli, Proteus vulgaris, Salmonella typhimurium, Shigella dysenteriae and Klebsiella pneumoniae. Orange seed powder produced the greatest reduction among the individual seed treatments, reducing TVC and TCC by 35.23% and 72.30%, respectively, while MgONPs produced larger inhibition zones than the individual seed powders. Selected multi-component treatments demonstrated greater antibacterial effectiveness. None of the five target bacteria was recovered following MgONP–pawpaw, moringa-MgONP-pawpaw, pawpaw-MgONP-orange or complete moringa-pawpaw-MgONP-orange treatment. The complete treatment produced the lowest TVC and TCC values of 2.67 ± 0.58 and 1.00 ± 1.00 CFU/mL, corresponding to reductions of 98.96% and 99.17%, respectively. It also produced large inhibition zones and low MIC and MBC values. The findings indicate that selected seed powder-MgONP combinations are promising treatment or pretreatment materials for bacterially contaminated water. Further optimizations and safety assessment are required before practical application.