This research proposes an integrated framework to investigate human-dominated systems and provide a basic approach to urban and regional studies in which the multiple interactions between economic and ecological processes are considered as a whole. Humans generate patterns of land use, infrastructures and other settings and redistribute ecosystem functions as flows of energy and matter for self-maintenance. To understand these emerging interactions between humans and ecological processes, human activities (e.g. transformation processes, land conversions, use of resources) and biophysical agents such as geomorphology, climate and natural cycles need to be considered. Emergy Analysis (spelled with an “m”) is then used as an environmental accounting method to evaluate different categories of resource use with reference to their environmental cost. A case study of the Province of Cagliari (in the island of Sardinia, Italy) is reported and the procedure for allocating emergy flows, assigning them to districts and managing point data is discussed. Outcomes plotted on a map showed non-homogeneous spatial distribution of emergy flows throughout the region, suggesting the way ecosystem functions are affected and restructured by the human economy.