There have been numerous studies focused on the effect of water on asphalt mixtures, the mineralogy of the aggregates, mastic, and voids. In this research, the effect of water on binder is evaluated in the context of chemical changes, and how such changes impact the material rheological response of asphalt mixtures. This phenomenon has impact on the durability of pavement insomuch as water affects our roads due to prolonged periods of rain and high relative humidity; a typical characteristic of tropical countries. The procedure applied in this research was to submerge 2 mm thick sheets of asphalt in water (of constant controlled properties) for twenty-one (21) months. During that time, the progressive changes in chemical properties, physical properties, and performance of the asphalt were tracked. The results presented in this article are focused on the analysis of the asphalts’ activation energy (and the generated change during the period of submersion) in relation to its response to the Multiple Stress Creep and Recovery (MSCR) test: one of the rheological tests that effectively represents the asphalts’ behavior under different stress and strain levels.