Abstract Transboundary water relations in the Euphrates–Tigris (ET) basin are often marked by political confrontation and rivalry between Iraq, Syria and Turkey. Even in the absence of political stability, riparian states have remained in contact with one another over the ET rivers at different levels by establishing and revitalizing joint governance mechanisms. In these processes, multiple actors—ranging from bureaucracies and heads of state and government, to epistemic communities—have focused on cooperative socio-economic development aspects of otherwise divisive water-related matters in the basin. Hence, the article aims to examine various emerging actors and mechanisms, arguing that their co-existence in the basin demonstrates a case of ‘imperfect peace’. Since the invasion of Iraq in 2003 and with the start of the domestic unrest in Syria in 2011, transboundary water relations in the basin have been carried out within the context of an unstable international security environment, particularly with the emergence of the non-state armed groups who have used water as a weapon against their opponents. The article therefore addresses policy-relevant research questions, such as what kind of joint security mechanism the riparian states should create to cope with violent non-state actors who control water and infrastructure under the conditions of ‘imperfect peace’. In the same vein, the article analyses the strategic role that water plays in environmental peacebuilding and discusses the possible ways and means to improve the protection of water during and after armed conflicts.