Increasing pressure on mountain water resources is making it necessary to address water governance issues in a transdisciplinary way. This entails drawing on different disciplinary perspectives, different types of knowledge, and different interests to answer complex governance questions. This study identifies strategies for addressing specific challenges to transdisciplinary knowledge production aiming at sustainable and reflective water governance. The study draws on the experiences of 5 large transdisciplinary water governance research projects conducted in Austria and Switzerland (Alp-Water-Scarce, MontanAqua, Drought-CH, Sustainable Water Infrastructure Planning, and an integrative river management project in the Kamp Valley). Experiences were discussed and systematically analyzed in a workshop and subsequent interviews. These discussions identified 4 important challenges to interactions between scientists and stakeholders—ensuring stakeholder legitimacy, encouraging participation, managing expectations, and preventing misuse of data and research results—and explored strategies used by the projects to meet them. Strategies ranged from key points to be considered in stakeholder selection to measures that enhance trustful relationships and create commitment.