Mesopotamia is often regarded the “cradle of civilization.” The development of water management practices in the region is thought to have played a key role in the emergence of these early civilizations. We present the first direct dating of a palaeo-canal system at the ancient city of Girsu, Mesopotamia (modern Iraq) (occupied between 4800 and 1600 BC). We describe the use of archaeological and radiocarbon (14C) dating techniques to establish the age of this canal system. Our results show considerable differences between shell 14C dates on the one hand and charcoal 14C dates and archaeological evidence on the other. This likely reflects the impact of freshwater reservoir effects from the Tigris and Euphrates Rivers. Although the FRE from rivers is widely acknowledged, its impact on 14C dates in Mesopotamia is rarely discussed and poorly understood. Our results provide a first indication of its variability and magnitude. With the publication of our results we aim to highlight the problem and re-initiate collaborative research efforts in improving 14C dating in this important region.