Water scarcity has various negative side-effects on river ecosystem and riverine biodiversity with the deteriorated water quality and quantity. Due to global climate change, a continuous increase in the proportion of intermittent rivers and aquifers is envisaged that will make them the dominant water bodies in the Mediterranean basin. To our best knowledge, hydrological, physico-chemical and ecological processes in intermittent rivers are scarce and not sufficiently supporting specific management options under the characteristic flush and drought conditions of intermittent rivers. The INWAT project aims at estimating intermittent river and groundwater quality and evaluating environmental problems associated to water scarcity in the seven Mediterranean catchments (Spain, France, Italy, Turkey, Jordan, Tunisia, Algeria) representing a wide range of management scenarios to ensure the transferability and further impact of the developed decision-support system from EU members to EU associated and MENA countries. Specific objectives are: (i) To develop innovative methods for hydrological monitoring and innovative hydrological modelling tools tailor-made to intermittent rivers representing the widest possible diversity of management scenarios under water scarcity conditions, such as sea intrusion and groundwater recharge, groundwater water quality issues. (ii) To improve the knowledge and capacity on pollution sources and processes naturally attenuating contamination by chemicals in intermittent rivers and aquifers. (iii) To develop methodologies for monitoring and assessing the ecological status of intermittent rivers with a particular focus on the development and refinement of novel biological indicators including metagenomic approaches. (iv) To develop a decision-support system with stakeholders involved in water management for the design of management actions to help minimizing and mitigating the effects of global change in water-scarce regions.