Intermediate cities in Asia and Africa house more than 60% of the world’s urban population. More than 54% of the people here face high levels of water stress and are increasingly vulnerable to water-related risks such as floods, limited access to safe drinking water and water pollution. These urban water risks are complex outcomes of climate change, land use changes, governance failures, and social inequities. This study examines the co-evolution of three water risks and governance responses through the case of Guwahati, India. Guwahati, on the Brahmaputra River in the Northeast of India, serves as a case of an intermediate city to demonstrate changes in water risk governance trends. We focus on studying the connected governance responses to changes in three interrelated water risks, i.e., domestic water supply, urban floods, and river pollution. The shifts in the socio-political structures for these risks are assessed by combining historical institutionalism with multi-level perspective theory. The results show that despite the growing diversity of actors and devolution of responsibilities in cities to mitigate water risks, there is an ongoing tug-of-war between centralized and decentralized modes of decision-making. Contrary to the recommendations for decentralized urban governance, the trend is currently tugging towards a centralized decision-making mode. However, when differences arise between the local and national, local actors within their limited frames of action manage to circumnavigate nationally dictated mandates to fit local needs.