Maputo, Mozambique’s capital city, is marked by clear socio-spatial divisions in access to sanitation services and distributions of environmental risks. Current development plans tend to reproduce these inequalities and suggest that some residents’ sanitary needs are more important than others. We contest this logic of differentiation underpinning current interventions in Maputo, revealing how the assumption of different sanitary needs has become normalized and naturalized in the urban environment. We use a genealogy of sanitation in Maputo and the former colonial city of Lourenço Marques to trace how colonial power relations worked to normatively distinguish urban spaces and the people who live in them, making some residents and places more deserving of public protection and investments than others. Drawing on Foucauldian theorizations of governmentality, we analyse colonial authorities’ sanitary plans and interventions to show how differences and separations between spaces and bodies were and are produced. Projects of drainage and land reclamation created clean, dry and sanitary habitats for the privileged white few, the existence of which simultaneously created the wet, unhealthy and muddy spaces deemed good enough for the non-white majority. Such manufactured spatial distinctions, in turn, worked to strengthen the perception of differences in cleanliness between people. These differences were consequently mobilized by the Lourenço Marques health service to further mark and legitimize racial segregation. This is how social and spatial inequalities became naturalized in the urban environment over time, culminating in the stark sanitary divides that continue to mark the contemporary city.