Recent fossil discoveries of early cetaceans and sirenians document the functional transitions that occurred as each group adapted to a completely aquatic existence, but the timing and path of their ecological transition remain uncertain. We analyzed the stable-isotope composition of tooth enamel from several early members of each group to reconstruct the dietary, foraging, and habitat preferences of basal taxa. Carbon isotope (δ13C) values provided evidence of foraging within freshwater, terrestrial, and marine environments, including seagrass beds, whereas oxygen isotope (δ18O) variation was used as a measure of commitment to aquatic habitats. Enamel samples were collected from four regions (south Asia, north and west Africa, and southern Europe) spanning the late early Eocene (ca. 53.5 Ma) to the late Eocene (ca. 36 Ma). Sirenian and cetacean taxa included species that were likely capable of some terrestrial locomotion, and more specialized forms that were morphologically fully aquatic. Cetacean δ13C and δ18O values indicate that some early members of this group (some pakicetids) inhabited freshwater environments, but later members (e.g., remingtonocetids, protocetids, and basilosaurids) moved quickly into estuarine and marine environments. Low δ18O variation confirms that all of these early forms were primarily aquatic, but δ13C and δ18O values for early sirenians indicate an early transition to a marine seagrass diet without any evidence of an intermediate connection to freshwater habitats.