Technical Abstract: The thermal environment of seedlings changes significantly over diurnal and seasonal time scales. Early-season thermal stress delays emergence in cotton and has subsequent effects on yield and fiber quality. In this study, a biochemical analysis of the thermal dependence of metabolism in preemergent seedlings identified sources of thermal limitations that were used as the basis for computer modeling of the thermal dependence of metabolism. The optimal thermal range for seedling metabolism was used in the analysis of the patterns and magnitude of thermal stresses. Data visualization techniques were used to qualitatively analyze the thermal environment and the predicted thermal stresses on the plant. Alterations in the thermal dependence of a seedling enzyme were modeled and demonstrate the utility of such an approach to the alleviation of thermal stress. Several management scenarios involving irrigation frequency and row spacing were shown to alter the pattern of thermal stresses.