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Hot water treatment (HWT) is a versatile technique for synthesizing metal oxide nanostructures (MONSTRs) by immersing metal substrates in hot water, typically in glass beakers. The proximity of substrates to the heat source during HWT can influence the temperature of the substrate and subsequently impact MONSTR growth. In our study, zinc (Zn) substrates underwent HWT at the base of a glass beaker in contact with a hot plate and at four different vertical distances from the base. While the set temperature of deionized (DI) water was 75.0 °C, the substrate locations exhibited variations, notably with the base reaching 95.0 °C. Scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), X-ray diffraction (XRD), and Raman spectroscopy showed stoichiometric and crystalline zinc oxide (ZnO) nanorods. ZnO rods on the base, exposed to higher temperatures, displayed greater growth in length and diameter, and higher crystallinity. Nanorods with increasing vertical distances from the base exhibited a logarithmic decrease in length despite identical temperatures, whereas their diameters remained constant. We attribute these findings to crucial HWT growth mechanisms like surface diffusion and “plugging”, influenced by temperature and water flow within the beaker. Our results provide insights for optimizing synthesis parameters to effectively control MONSTR growth through HWT.