The analysis of carbon isotope discrimination (Δ¹³C) in crop plant remains from seven Bronze Age sites in northern Mesopotamia and the Levant shows clear differences in water availability between the different geographic areas and throughout the different periods (3000–1200 BC). Amongst the different moisture variables modelled precipitation minus evaporation (P-E—using a macrophysical climate model (MCM)) results in very high correlation (0.74) with Δ¹³C values in barley, supporting the significance of climate parameters (effective moisture) in carbon fixation in this species. The comparison of Δ¹³C values of different crops in different periods confirms increased aridity during the Middle Bronze Age (2000–1600 BC), compared to the later Early Bronze Age (2700–2000 BC) particularly in the north-eastern Syrian territory with generally lower Δ¹³C values during the Middle Bronze Age, as has been documented in palaeoclimate proxies, and in agreement with the MCM. Standard deviation in Δ¹³C values from grains or seeds of one species originating from different samples of an individual site may be understood as variability in moisture conditions during the grain-filling period around the considered location. Large standard deviations occur preferably in sites with low mean annual precipitation (e.g. at Emar) and suggest that in these sites, at least some of the crops were irrigated.