The transformation of urban sanitation is critical to achieving sustainable development. However, recent research challenges the assumption that the networked sanitation systems of the industrialized world are universally desirable. Instead, there is a growing call for practice-oriented scholarship and policy-making that start with an analysis of what people actually do in their everyday lives as they interact with differentiated, decentralized, or alternative sanitation infrastructures. This paper explores the relationship between sanitation infrastructures and socio-political urban geographies, and investigates how sanitation practices are shaped by and, in turn, shape human ecosystems in rapidly urbanizing contexts. We propose a refined human ecosystem framework (HEF) that foregrounds the role of embodied practices in mediating between material and social domains within the unequal, politicized, and contentious processes of urban metabolism. Using contemporary Shanghai as a case study, we examine the socio-material-temporal characteristics of existing sanitation practices and their connections to heterogeneous sanitation infrastructures. Through this, we demonstrate how cultural beliefs and social norms shape infrastructure functionality and the broader sustainability of sanitation systems. This paper contributes to the ongoing debate on the politics of sanitation infrastructure and highlights the need for context-specific approaches to sanitation planning and implementation that center on local practices.