The term of nanotechnology has emerged recently in several fields of interest that refers to the researches and innovations that are concerned with making materials on a very small size close to the scale of atoms and molecules. In the present work, the effects of green synthesis of different nanoparticles on the quality of irrigation water, the availability of some heavy metals content in soil and the plant, and the productivity of Marjoram were studied in detail. The obtained results showed that the addition of nanoparticles (NPs) materials has resulted in noticeable variations in the removal percentages of Cu and Fe from aqueous solution. The maximum values obtained for adsorption of Cu (II) on ZnO, MgO, and SiO2 NPs, within pH (3–5) were 89.9%, 83.3%, and 68.36%, respectively. Whereas, the maximum adsorption values of Fe (III) at pH 3.3 were 82%, 80%, and 65% for ZnO, MgO, and SiO2 NPs, respectively. It was clearly seen that the effective of NPs application on reduction of the available Cu in the studied soil samples. The order of sequence for the effects of NPs application was found to take the following order Zn2 > Zn1 > Mg2 > Si2 > Mg 1 > Si1 > C (control). The highest values of the available Cu were observed in the control treatment, whereas the lowest values were obtained when Zn2 was added, and the same tendency was observed with the substantial concentrations of Fe. The addition of NPs to the soil samples had positively affected the Cu uptake via plant. The effects of NPs and the additions of Cu and Fe on the availability of NPK in the soil system were very completed and osculated from one treatment to another. The same tendency was observed with the total concentration of NPK in the plant.