Efficiently-loaded, controlled-release nanofertilizer systems improve fertilizer use efficiency, germination percentage, root and shoot length, seedling growth, and can overcome the problem of the ever-increasing cost of agrochemicals and their inherent post-application losses, which lead to severe soil, water, and eatable commodity pollution. In this study, magnetized distilled waters (MDWs) with various physicochemical characteristics have been used to enhance the urea loading efficiency into mesoporous nano silica (mNS). The mNS was in-house synthesized by a sol-gel method and characterized by UV-visible spectrophotometer (UV-Vis), Fourier Transform Infrared Spectroscopy (FTIR), Energy-dispersive X-ray (EDX) spectroscopy, X-ray powder diffractometer (XRD), and thermogravimetric (TGA)/differential thermal analyzer (DTA) and Field Emission Scanning Electron Microscope (FESEM). We then compared the effects of magnetized and normal water, mNS, urea-loaded mNS, and bare urea on the germination of wheat seeds under laboratory conditions. Comparing to mNS in DW, we detected an increase in root (4-fold) and shoot (1.85-fold) lengths when using mNS in MDW. The root and shoot length in case of urea loaded mNS in normal DW and MDW were 2.05 and 1.77 times more, respectively. The germination percentage and root and shoot length increased significantly in accordance to the exposure to 0.5% (w/v) mNS in magnetized water (mNS-MDW) and urea loaded mNS in magnetized water (mNSU-MDW) as compared to same treatment with mNS in distilled water (mNS-DW). Our findings show that the unfavorable effects of urea fertilizer on seed germination, seedling growth, and early plant growth on paper towels can be ameliorated, at least partially, by supplementation with mNSU-MDW. We conclude that mNS-MDW and mNSU-MDW might be effective alternatives for sustained and effective means of fertilizer use efficiency during wheat seed germination.