Water stress in Mediterranean countries is the result of both variable and changing climatic conditions and widespread anthropogenic pressures. Evrotas, an intermittent river located in Southern Greece, was used as a case study to assess the impacts of water stress on Mediterranean lotic ecosystems. Based on hydrological analyses, it was revealed that during prolonged drought years, such as the summers of 2007 and 2008, the vast majority of the Evrotas riverbed was completely desiccated, primarily as a result of substantial water abstraction for irrigation. The effects of desiccation on the riverine ecosystem were evaluated using fish and macroinvertebrate assemblages according to the demands of the Water Framework Directive 2000/60/EC (WFD). Faunal responses to water stress were assessed through comparisons of assemblages attributes in perennial and intermittent reaches and pre-drought versus postdrought communities. Effects of hydrological disturbance on fish species richness, density, percentage composition and size structure were more pronounced in intermittent than in perennial sites. The most obvious and immediate impact was the elimination of populations in the intermittent reaches. However, upon flow resumption, the recolonisation from upstream perennial reaches began, thereby permitting partial re-establishment of the depleted fish communities. Nevertheless, the structural integrity of fish communities remained severely impacted and recovery was markedly slow. On the contrary, post-drought macroinvertebrate assemblages were not affected by summer droughts, and the recruitment processes were rapid after flow resumption. Our findings point to the necessity of establishing a distinction between naturally and artificially driven intermittent rivers. We, therefore, propose the introduction of an ''artificially intermittent Mediterranean river'' condition within the context of the WFD assessment applications.