This study investigates the chemical structure of profoxydim, focusing on its E–isomer, the main commercial form. The research aimed to determine the predominant tautomeric forms under various environmental conditions. Using proton and carbon–13 NMR spectroscopy alongside theoretical modeling, we examined tautomers and their conformers in different solvents (MeOD, DMSO, CDCl3, benzene) to mimic gas and aqueous phases. The findings reveal that the enolic form dominates in the gas phase, while the ketonic form prevails in aqueous environments, providing key insights into the herbicide’s environmental behavior. We also observed an isomeric transition from E to Z under acidic conditions, which could affect profoxydim’s reactivity in natural environments. The theoretical calculations indicated that in acidic conditions, the E and Z forms are nearly degenerate, with the E form remaining dominant in neutral environments. Additionally, QSAR models assessed the toxicity of various tautomers, revealing significant differences that could impact bioactivity and environmental fate. This research offers crucial insights into the structural dynamics of profoxydim, contributing to cyclohexanedione chemistry and the development of more effective herbicides.