This is a first-time assessment of the direct and indirect effects of hydrothermal conditions on pathogenesis of root infections in cultivated varieties of spring wheat and barley. Long-term field research (2000–2015) was carried out in the area of risk farming combined with laboratory experiments. The effects of the phytosanitary condition of soil, seeds, and underground plant organs were taken into account. It was found that soil pathogenic population and the development of soil-borne infections largely depend on hydrothermal factors. The development of root rot of spring wheat was stimulated by arid conditions during tillering and heading: the disease rate was increased by 33.5% compared to the optimal moisture supply against a background of a high plant pathogen population of the soil. In drought conditions, the number of saprotrophic microorganisms decreased 3.3 times and suppressive soil activity fell 3.0 times provoking root infections. Microorganisms consuming inorganic forms of nitrogen and cellulolytic agents were found to be highly sensitive to hydrothermal factors. Arid conditions increased the plants’ susceptibility to the inoculum of soil origin, since the increase in the number of conidia in the inoculum from 5–15 to 150–180 per 1 g of soil increased the frequency of infections by root rots by 7.8 times, especially on the epicotyl and the base of the stem. Damage of root rot was increased by pest flies Oscinella frit L., O. pusilla Mg., Phorbia genitalis Schnb., and Mayetiola destructor Say. Their activity increased in warm, arid conditions. Drought-resistant gramineous weeds Panicum miliaceum ssp. ruderales L. (Kitag.) Tzvei., Setaria glauca (L.) Beauv., Avena fatua L., Setaria viridis (L.) Beauv. competed with the crop and consequently increased the development of root rot by 20% or more in dry years. Seeds of gramineous weeds, multiplied after dry years, contributed to reproduction and survival of many soil-borne phytopathogens. Grain ripening in moistened conditions led to transmission of the root rot agents Bipolaris sorokiniana Sacc. Shoem. (syn. Helminthosporium sativum Pam., King et Bakke) and Fusarium fungi via seeds. This led to proliferation of root rot in the germination phase and significantly (53%) affected the cereals’ germ.