Research in urban political ecology has been important in recent decades in understanding the complex socionatural processes entailed in urbanization, exploring the local and global linkages of the production and consumption processes of urban metabolism. While these studies have explored diverse networks and artefacts in this metabolism, little attention has been paid to the flows of the pollution of water and air, particularly of the industrial emissions that are also key to the socionatures of urbanization in industrialized regions of the Global South. In this paper, we explore two interconnected nodes in the metabolism of the Guadalajara Metropolitan Area in Western Mexico. These are key sites for the flows of resources and emissions, with different levels of social discontent and conflict related particularly to the health impacts of water pollution. Here, government authorities tend to deflect attention from industrial- and city-level sources of pollution, focusing instead on proximate sources and household emissions. Organized social resistance, on the other hand, calls attention to powerful industrial actors and speculative urban development while taking action to imagine new socio-ecological configurations in the region. We focus on the role of the state in maintaining socio-ecological inequities, and the lessons that can be learned about urban metabolism by expanding the frame to include industrial processes in the shaping of urban socionatures.