A capacity building workshop was held in Chiang Mai, Thailand, 21–23 January 2013 to help increase understanding of the implications of analytical and normative uncertainties associated with climate change and other large-scale drivers for the governance of trans-boundary river basins. The mix of participants in terms of countries, expertise and disciplines allowed for a critical perspective on issues in several key transboundary river basins including the Indus, Ganges, Brahmaputra and Mekong. The deliberations underlined that in Asia, complex power relations demand explicit consideration of normative uncertainty in addition to the conventional focus on analytical uncertainty. Power imbalances, for instance, were noted as an important barrier to the flow of information and sharing of data, which increases uncertainty. It was recognized that it is often easier and more appropriate for negotiations to focus on sharing the benefits of water than just on the allocation of physical water flows. Participants and trainers jointly developed a set of propositions on uncertainty and the governance of transboundary river basins under a changing climate and committed to completing a co-authored synthesis article around some of these.