In Near Eastern archaeology, studies on crop management during the early stages of civilisation have been based on cuneiform texts and only recently have geoarchaeological surveys and archaeobotanical studies tried to identify agricultural practices. Nevertheless, direct evidence for irrigation and water management is very rare and difficult to interpret. New possibilities for analysing these ways of management have been provided by stable carbon isotope analysis of ancient crops. In this study carbon isotope discrimination (Δ13C) was performed to assess the growing conditions of fossil cereal grains. Charred grains of emmer and barley recovered from the same site, Arslantepe in eastern Anatolia, over a 1,000 years long continuous sequence during the third millennium b. c. have been analysed and compared. The variation in water availability during grain filling, estimated by Δ13C, can be attributed to climate change and/or human practices. Distinguishing exactly which is to blame is complex but essential in reconstructing specific management practices. Variations in the 13C/12C ratio suggest that barley and emmer grew under different water regimes. In particular, a different management system was adopted between 3000 and 2800 cal. b. c. when emmer was sustained by human-induced water supply, whereas the more resistant barley was rain-fed and possibly assigned to more marginal terrains. Our results are compared with the stable carbon isotope data available for other Near Eastern sites. Emmer and barley records are also compared with deciduous oak Δ13C from Arslantepe in order to better understand the influence of environmental factors, climate and human impact.