Water scholars and practitioners generally agree that improving water governance is the key to addressing water insecurity in developing countries. We review the literature on water governance and argue for a second-generation research agenda, which pays more attention to the study of incentive structures, is multi and inter-disciplinary in orientation and with clear policy implications. We then illustrate how theories drawn from public economics, new institutional economics, political economy and public administration can help diagnose the challenges of integrated water resources management, improving efficiency of water utilities, privatization of utilities and public-private partnerships, water pricing reforms, virtual waters/water trading, among others. We conclude that these tools can help advance the second-generation research agenda on water governance.