This study aimed to evaluate the effects of the Martil River rehabilitation project and recently constructed dam infrastructures to reduce flood risks and to promote local socio-economic development on the ecological integrity of the river. The assessment focused on changes in fluvial landforms over time and the evaluation of aquatic ecosystems based on six physicochemical parameters (temperature, pH, electrical conductivity, dissolved oxygen, biochemical oxygen demand, and chemical oxygen demand), morpho-hydrological variables (stream width, water depth, and current speed), habitat indices (QBR, IHF, and MQI), and macroinvertebrate assemblages of EPT, OCH, and Chironomidae (Diptera) at five stations from autumn 2015 to spring 2018 (prior to and during the rehabilitation actions). The results showed that the river rehabilitation project led to profound changes in Martil River’s ecosystem and water quality over time. Physicochemical and habitat measurements at the rehabilitated sites revealed a major change in macroinvertebrate communities due to changes in fluvial landforms in relation to flow-sediment regimes. As a result, some typical species of lentic habitats disappeared, while alien, opportunistic, and lotic species appeared.