The co-creation of knowledge through a process of mutual learning between scientists and societal actors is an important avenue to advance science and resolve complex problems in society. While the value and principles for such transdisciplinary water research have been well established, the power and empowerment dimensions continue to pose a challenge, even more so in international processes that bring together participants from the Global North and Global South. We build on earlier research to combine known phases, activities, and principles for transdisciplinary water research with a negotiated approach to stakeholder empowerment. Combining these elements, we unpack the power and empowerment dimension in transdisciplinary research for peri-urban groundwater management in the Ganges Delta. Our case experiences show that a negotiated approach offers a useful and needed complement to existing transdisciplinary guidelines. Based on the results, we identify responses to the power and empowerment challenges, which add to existing strategies for transdisciplinary research. A resulting overarching recommendation is to engage with power and politics more explicitly and to do so already from the inception of transdisciplinary activities as a key input for problem framing and research agenda setting.