Human niche construction theory is an interesting mode of analysis that centres on the thesis that humans and other species modify their environment and in doing so alter the evolution of their descendants (Laland et al., in Philos Trans R Soc B 366:927–934, 2000). The construction of irrigation systems is one example of a large-scale modification to the landscape carried out in the ancient Near East. In this article it will be investigated whether the creation of an irrigation system has indeed resulted in an altered evolution of the inhabitants of the system. The irrigation system of the Zerqa Triangle in the Jordan Valley forms an excellent case study as the system has been used intermittently over the last 4000 years. While human niche construction is difficult to prove for the more distant periods, sufficient information is available for the early modern period to suggest that the irrigation system was one of the factors that caused a spatially restricted, hierarchical clan-based social organisation that resulted in endogamy and genetic disease.