Urban areas are understood to be extraordinarily spatially heterogeneous. Spatial heterogeneity—and its causes, consequences, and changes—are central to ecological science. The social sciences and urban design and planning professions also include spatial heterogeneity as a key concern; however, urban ecology, as a pursuit that integrates across these disciplines, lacks a theoretical framework that synthesizes the diverse and important aspects of heterogeneity. We present the concept of dynamic heterogeneity as a tool to explore how social and ecological heterogeneities interact and how, together, they serve as both an outcome of past interactions and a driver of future heterogeneity and system functions. To accomplish this goal, we relate heterogeneity to the fundamental concept of the human ecosystem. The human ecosystem concept identifies key processes that require operationalized models of dynamic heterogeneity in three process realms: the flow of materials, the assembly of urban ecosystem biota, and the locational choices humans make concerning land. We exemplify a specific dynamic model of heterogeneity in each of these realms and indicate a range of complementary statistical approaches to integrate the drivers and outcomes of dynamic heterogeneity across the three realms. We synthesize a hierarchical framework for a theory of dynamic urban heterogeneity, noting its complementarity to other major urban theories and general model approaches. We hypothesize that human actions and structures amplify the dynamics of heterogeneity in urban systems.