Complex networks analyses of many physical, biological and social phenomena show remarkable structural regularities, yet, their application in studying human past interaction remains underdeveloped. Here, we present an innovative method for identifying community structures in the archaeological record that allow for independent evaluation of the copper using societies in the Balkans, from c. 6200 to c. 3200 BC. We achieve this by exploring modularity of networked systems of these societies across an estimated 3000 years. We employ chemical data of copper-based objects from 79 archaeological sites as the independent variable for detecting most densely interconnected sets of nodes with a modularity maximization method. Our results reveal three dominant modular structures across the entire period, which exhibit strong spatial and temporal significance. We interpret patterns of copper supply among prehistoric societies as reflective of social relations, which emerge as equally important as physical proximity. Although designed on a variable isolated from any archaeological and spatiotemporal information, our method provides archaeologically and spatiotemporally meaningful results. It produces models of human interaction and cooperation that can be evaluated independently of established archaeological systematics, and can find wide application on any quantitative data from archaeological and historical record.