In this work, two case studies were studied: Querétaro (Bajio) and the State of Mexico (Edomex). Both states are part of the Sierra Madre Occidental, where temperate and subhumid climates are experienced in both states. The surface soils are predominantly Leptosols in the Bajio and Andosols-Feozems in the Edomex. The dynamic mobility of water and fertilizers is associated with humic substances, mineralogical phases, metal dispersion, pore type, pore volume, and thermal behaviour. Both agricultural soils exhibited high porosity and surfaces with co-dispersion of Al3+/Si4+ and Ti4+/Fe2+,3+ ions and mixed mineralogical phases such as montmorillonite, anorthite, quartz, magnetite, goethite, hematite, and kaolinite. On the one hand, the C/N values for the Bajio-crop and Edomex-crop soils showed values of 15 and 11, respectively. On the other hand, the Bajio-crop and Edomex-crop soils showed C/O values of 0.38 and 0.42, respectively, indicating the accumulation of organic carbon and the presence of various humic substances. Finally, the Bajio-crop soil presented a higher surface area, pore diameter, and pore volume than the Edomex-crop soil, which is associated with greater adsorption and nutrient retention. On the contrary, the Edomex-crop soil presented greater thermal resistance than the Bajio-crop soil, which is associated with a better capacity for heat dissipation during irrigation processes or fertilizer application.