Crude oil pollution of water bodies is a worldwide problem that affects water ecosystems and is detrimental to human health and the diversity of living organisms. The objective of this study was to assess the ability of water hyacinth (Eichhornia crassipes (Mart.) Solms) combined with the presence of magnetic nanoparticles capped with natural products based on Myrrh to treat fresh water contaminated by crude petroleum oil. Magnetic nanoparticles based on magnetite capped with Myrrh extracts were prepared, characterized, and used to adsorb heavy components of the crude oil. The hydrophobic hexane and ether Myrrh extracts were isolated and used as capping for magnetite nanoparticles. The chemical structures, morphologies, particle sizes, and magnetic characteristics of the magnetic nanoparticles were investigated. The adsorption efficiencies of the magnetic nanoparticles show a greater efficiency to adsorb more than 95% of the heavy crude oil components. Offsets of Water hyacinth were raised in bowls containing Nile River fresh water under open greenhouse conditions, and subjected to varying crude oil contamination treatments of 0.5, 1, 2, 3, and 5 mL/L for one month. Plants were harvested and separated into shoots and roots, oven dried at 65 °C, and grounded into powder for further analysis of sulphur and total aromatic and saturated hydrocarbons, as well as individual aromatic constituents. The pigments of chlorophylls and carotenoids were measured spectrophotometrically in fresh plant leaves. The results indicated that the bioaccumulation of sulphur in plant tissues increased with the increased level of oil contamination. Water analysis showed significant reduction in polyaromatic hydrocarbons. The increase of crude oil contamination resulted in a decrease of chlorophylls and carotenoid content of the plant tissues. The results indicate that the water hyacinth can be used for remediation of water slightly polluted by crude petroleum oil. The presence of magnetite nanoparticles capped with Myrrh resources improved the remediation of water highly polluted by petroleum crude oil.