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Over the last 8000 years the Fertile Crescent of the Near East has seen the emergence of urban agglomerations, small scale polities and large territorial empires, all of which had profound effects on settlement patterns. Computational approaches, including the use of remote sensing data, allow us to analyse these changes at unprecedented geographical and temporal scales. Here we employ these techniques to examine and compare long term trends in urbanisation, population and climate records. Maximum city size is used as a proxy for the intensity of urbanisation, whilst population trends are modelled from settlement densities in nine archaeological surveys conducted over the last 30 years across the region. These two measures are then compared with atmospheric moisture levels derived from multiple proxy analyses from two locations close to the study area, Soreq Cave in Israel and Lake Van in south-eastern Turkey, as well as wider literature. The earliest urban sites emerged during a period of relatively high atmospheric moisture levels and conform to a series of size thresholds. However, after the Early Bronze Age maximum urban size and population levels increase rapidly whilst atmospheric moisture declines. We argue that although the initial phase of urbanization may have been linked to climate conditions, we can see a definitive decoupling of climate and settlement patterns after 2000 BC. We relate this phenomenon to changes in socio-economic organisation and integration in large territorial empires. The complex relationships sustaining urban growth during this later period resulted in an increase in system fragility and ultimately impacted on the sustainability of cities in the long term.