In the last decades, thousands of socio-environmental conflicts have spawned, especially at the sub-national scale. Among these, water conflicts are especially complex and multifaceted, since most are driven by a combination of socio-economic dynamics that increase pressure on natural resources, more extreme hydro-climatic trends, outdated or biased legal frameworks, large power asymmetries between actors, and the dominance of sociotechnical paradigms that reduce the decision space of water policies. Although water conflicts often receive a lot of attention, public scrutiny, and media exposure, this has not necessarily transcended into improving our understanding of their relation to the coupled human-water systems in which they are embedded, and even less of their transformative potential to open the decision space on the development pathways of cities and water systems. Furthermore, if a conflict drags on, it creates the notion of conflict impasse, of a static nature and confined to a narrowed space. This can further obstruct our understanding of what the conflict is really about, what are its root causes, what are the motivations of key actors, how do actors mobilize different capitals to achieve their goals and coalesce in networks, and what are the best ways to move forward and find transformative alternatives. This PhD thesis aims to reveal that water conflicts are highly dynamic and the result of a complex web of events influenced by social and natural long-term dynamics, knowledge controversies, and actors and network dynamics that widen the perception of the boundaries of water conflicts. To map out and navigate these turbulent waters of water conflicts, new transdisciplinary methods and action research are necessary. The realization that conflicts are complex and dynamic, and that transdisciplinary and action methods are needed to transform them has many implications. First, given the longterm dynamics that determine a conflict, it is necessary to analyze its history beyond the “official” start of the conflict, even before the involvement of the main actors in the conflict. Therefore, a water conflict involves much more than only just a dispute between parties, but also wider and more transcendent discussions of sustainability of cities and water systems and fairness of socio-political systems. Second, these long-term dynamics are both social and natural, thus, water conflicts need to be analyzed in an interdisciplinary manner to better deal with controversies composed of different kinds of uncertainties and ambiguity in the coupled human-water systems. The development of new hybrid disciplines like socio-hydrology and hydrosocial studies are a step forward, but they keep being dominated by either a natural sciences or social sciences epistemology. Third, further analyzing the conflict in a transdisciplinary and longitudinal manner, by involving actors in knowledge co-production, can improve our understanding of knowledge controversies, which in turn increases the reflectivity of the role of science and scientists in these conflicts.