Nanoparticle effects on mechanical and physical properties of soil have rarely been investigated, particularly those of iron and magnesium nano-oxides. This study investigated the effects of the application of nano-oxides on total porosity, mean weight diameter (MWD) of aggregates, volumetric water content at a matric potential of −100 kPa, penetration resistance, and saturated hydraulic conductivity. Nanoparticle type (two types comprising iron and magnesium nano-oxides), application dosage (four dosages of 0, 1, 3, and 5% by weight), and incubation period (40 and 100 days) comprised the factors considered. The magnesium nano-oxide treatments increased (P < 0.05) total porosity by reducing soil bulk density due to the smaller size of magnesium compared with iron by 0.04 cm3 cm−3. After both incubation periods, each application dosage of magnesium nano-oxide increased (P < 0.05) the MWD of the aggregates, ranging from 0.47 to 2.91, compared with the control and all of the iron nano-oxide dosages because of the large flocculation capacity of magnesium nano-oxide. The 1 and 3% applications of magnesium nano-oxide increased (P < 0.05) the water content, ranging from 0.01 to 0.02 cm3 cm−3 compared with the control and 1 and 3% of the iron nano-oxide dosages, possibly by increasing the specific surface, stabilizing the soil structure, and increasing the microporosity. Penetration resistance increased (P < 0.05) about 0.14–0.28 MPa under the iron nano-oxide treatments whereas penetration resistance decreased (P < 0.05) about 0.21–0.33 MPa under the magnesium nano-oxide treatments. The saturated hydraulic conductivity decreased (P < 0.05) after both incubation periods with iron (24–61%), and after incubation for 40 days with magnesium (38–56%). However, the saturated hydraulic conductivity increased (P < 0.05) from 46 to 61% after incubation for 100 days with magnesium. It was concluded that magnesium nano-oxides can improve selected soil physical and mechanical properties