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Intermittent (or temporary) rivers cease to flow every year or at least twice every five years. Such rivers drain large arid and semi-arid areas, covering approximately a third of the earth’s surface. The extent of temporary rivers is increasing, as many formerly perennial rivers are becoming temporary because of increasing water demand, particularly for irrigation. The combination of dry crusted soils and the highly erosive energy of the rain cause sediment resuspension and transport to the coastal areas. They are among the aquatic habitats most altered by human activities. During the summer even under no flow conditions the point sources are still active such as the wastewater effluents, resulting in nutrients and organic pollutants accumulating in the sediment. Sediment operates as a pollution inventory and pollutants are moved to the next basin with the first flush. Their vulnerability is intensified by the conflict between water use demand and aquatic ecosystem conservation. Advanced modelling tools have been developed to better describe intermittent flow dynamic changes such as the tempQsim model.