Objectives A contribution to the knowledge of the economy and the environmental surroundings of the populations living along the Nile valley in three different periods. Materials and methods This study reports stable isotope analyses on apatite bone samples of 139 humans, 48 mammals, and 43 fish from the Al Khiday archaeological sites in Sudan. The bones belong to four archaeological periods: pre‐Mesolithic, Mesolithic, Neolithic, and Meroitic. Data were processed statistically. Results A significant difference exists between the pre‐Mesolithic and Mesolithic mean δ18Ow value and the mean of the modern Nile. The mean δ18Ow values for the Neolithic humans and bovids are very similar (+1.5‰ ±4‰, and −2‰, respectively) and more positive than the mean values of Mesolithic mammals and Pre‐Mesolithic humans. The water ingested by Meroitic humans (+7‰ ± 2.5‰) is enriched in 18O in respect to the water ingested by the Neolithic population. There is a separation in the δ13Cdiet values between the pre‐Mesolithic humans (−14‰ ± 1‰) and Mesolithic mammals (−12‰ ± 2‰) group and the Neolithic humans (−18‰ ± 1‰), Meroitic humans (−19‰ ±1‰), Neolithic mammals (−21‰), and the modern (mean δ13Cdiet = −19‰ ±2‰) mammal group. Discussion The climate became warmer and more arid from the pre‐Mesolithic/Mesolithic to the Meroitic period. The environmental conditions influenced the strategies of subsistence and, in particular, the changes occurring from the pre‐Mesolithic to the Neolithic can be considered contemporaneous to the transition from hunting‐gathering‐fishing to cultivation‐herding. Am J Phys Anthropol 160:498–518, 2016. © 2016 Wiley Periodicals, Inc.