A novel treatment technique for produced water was developed using organic nanotubes (ONTs) as adsorbents. ONTs formed by the self-assembly of peptide lipids are known to adsorb heavy metals and hydrophobic molecules. Preferential adsorption of heavy metals against alkali- and alkali-earth metals above pH 6 was confirmed. Pb2+ in high-salinity model produced water was reduced to 0.04 ppm by treatment with ONTs, compared to 0.84 ppm without ONTs. The selectivity of Pb2+ against alkali-earth metals was over 3000. Design of the molecular structures of peptide lipids reduced the content of p-cresol in model produced water from 13 to less than 1 ppm. To improve separation from wastewater, ONTs hybridized with magnetic nanoparticles (MNPs) were obtained through the pH adjusting method. Hybrids maintained the hybridized state over a wide pH range (1-9). Adsorption tests using real produced water indicated that ONTs could adsorb heavy metals, suspended solids, oil, and some organic compounds in produced water in a one-step process, without pre-treatment.