Our central paradigm for urban ecology is that cities are emergent phenomena of local-scale, dynamic interactions among socioeconomic and biophysical forces. These complex interactions give rise to a distinctive ecology and to distinctive ecological forcing functions. Separately, both the natural and the social sciences have adopted complex system theory to study emergent phenomena, but attempts to integrate the natural and social sciences to understand human-dominated systems remain reductionist—these disciplines generally study humans and ecological processes as separate phenomena. Here we argue that if the natural and social sciences remain within their separate domains, they cannot explain how human-dominated ecosystems emerge from interactions between humans and ecological processes. We propose an integrated framework to test formal hypotheses about how human-dominated ecosystems evolve from those interactions.