The transformation of urban sanitation is critical to achieving sustainable development in the Global South. 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 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 as part of heterogeneous infrastructure configurations. 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 water and sanitation infrastructure in the Global South and highlights the need for context-specific approaches to sanitation planning and implementation that centre on local practices and knowledge.