Hydromorphological alterations are the most common pressures that occur in freshwater ecosystems, largely responsible for the overall decline of freshwater biodiversity. The EU 2030 Biodiversity Strategy, recognizing the crucial role of hydromorphological alterations, sets the target of 25 000 km of free flowing rivers in Europe by 2030. In this article, we discuss the hydromorphological restoration and mitigation measures in stream ecosystems implemented in Cyprus, the most arid country in the EU. We also assess their ability to contribute to the accomplishment of a free-flowing state, and we highlight the need for restoration guidelines for semi-arid areas in light of the climate crisis and the anticipated changes in water flow regimes. Our study showed that important progress has been made towards reconnecting streams in Cyprus, with the Water Framework Directive being the main driving force behind this effort. However, even in semi-arid areas with severe water scarcity, emphasis should be placed on the demolition of dams and other water storage obstructions, as they are primarily responsible for the interruption of stream continuity. Thus, the development of a prioritization tool is required. Although we focus on the hydromorphological restorations in Mediterranean streams, we argue that the issues raised in this paper concern other geographical regions and river types with similar flow regimes and future challenges.