The neonicotinoid insecticide thiamethoxam (TMX) is widely applied in agriculture, owing to its high spectrum of target pests. Its frequent use contributed to its accumulation in the environment, mainly in water; therefore, its natural degradation mechanisms are relevant to understand the physicochemical factors that can accelerate its decomposition. So, this study evaluated the stability of TMX against variations in pH, temperature, and exposure time to solar radiation, with the purpose of assessing the natural mechanisms of its degradation in water. Further, simulations of the reaction mechanisms at the molecular level were performed. It was observed that the degradation of TMX in the environment is favored by its exposure to solar radiation for several days and in more acidic pH conditions. However, TMX degradation did not result in reduced ecotoxicity. Basic pH values also help in the degradation of TMX, but by a lower percentage than that in an acid medium. Although exposure of TMX to solar radiation promotes heating of the compound, the isolated effect of thermal energy (temperature) is not sufficient for its degradation. The computer simulations showed the regions with higher electron densities and that the TMX structure is stable, preventing the bonds from breaking with increasing temperature, up to 60 °C. The HO− and H3O+ ions do not interact significantly with the molecule to the point of modifying its structure. With solar radiation, an electron can change to the excited state, contributing to TMX degradation due to a triplet configuration that allows it to react with the ions in the solution. In this way, the present work contributed to jointly present a theoretical and experimental study of the forms of natural degradation of the TMX contaminant.