Stable isotope analyses of human tooth enamel have allowed us to reconstruct the isotope composition of dietary carbon, changes in the oxygen isotope composition of drinking water and the possible migration of humans in ancient Terqa and Tell Masaikh (SE Syria). δ18Ocarbonate values of human tooth enamel from the interval comprising the Neo‐Assyrian to the modern Islamic periods (from 900 BC to AD 1949) generally mirror the isotope composition of Euphrates water, which is believed to have been a major drinking water source. Lower δ18Ocarbonate values of human Bronze Age apatite are linked to a different hydrologic system that was present in the Middle Euphrates valley at that time (2650–1700 BC). Higher δ18Ocarbonate values of some individuals in the Neo‐Assyrian (900–700 BC) and Islamic periods (AD 600–1200) may indicate human migration from the interior of the Near East. Low δ13Ccarbonate values (−11.3 to −12.4‰) of human tooth enamel from the interval comprising the Early Bronze to the Islamic periods (from 2650 BC to AD 1200) indicate C3 plants as a predominant source of dietary carbon. Changes in human dietary customs in SE Syria (with inferred usage of C4 plants) occurred in the modern Islamic period only (AD 1850–1949). Oxygen and carbon isotope data of sheep enamel show the usage of water bodies characterised by an enhanced evaporation rate during the Neo‐Assyrian time (900–700 BC) and grazing sheep herds on drier areas during the Islamic and the modern Islamic periods (after AD 600). Copyright © 2015 John Wiley & Sons, Ltd.