Markets for managing natural resources have existed for many decades and have gradually made their way into the mix of discourses on water policy. However, there are not many established water markets functioning worldwide and little understanding about how and why water markets emerge as allocating institutions. In order to understand the dynamics of the evolution of water markets, the experiences of selected cases with relatively mature water market systems were analyzed, namely: the Murray–Darling Basin in Australia; the Colorado-Big Thompson Project and the transfers between the Palo Verde and Metropolitan Water Districts in the USA; and Spain. We found that formal markets emerged in water scarcity situations where water rights already existed and were sometimes exchanged informally. Water markets have not always moved to reduce transaction costs, as some of those costs were necessary to achieve societal goals beyond economic efficiency. There is a significant difference between the idea of water markets as proposed by economic theory and actual practice in the water sector. As institutions, markets are humanly devised rules embedded in a social and political context and do not always lead to efficient or effective solutions for the management of resources.