A common belief is that, unlike today, ancient urban areas developed in a sustainable way within the environmental limits of local natural resources and the ecosystem's capacity to respond. This long-held paradigm is based on a weak knowledge of the processes underpinning the emergence of urban life and the rise of an urban-adapted environment in and beyond city boundaries. Here, we report a 6000-year record of environmental changes around the port city of Akko (Acre), Israel, to analyse ecological processes and patterns stemming from the emergence and growth of urban life. We show that early urban development deeply transformed pre-existing ecosystems, swiftly leading to an urban environment already governed by its own ecological rules and this, since the emergence of the cities.