A sediment bypassing plant based on innovative jet pump, ejectors, has been tested in the first-of-a-kind demo application at the harbor of Cervia (Italy, Northern Adriatic Sea). The ejector is a jet pump aimed to reduce sediment accumulation in navigation channels and coastal areas. Herein we present results of the first study assessing the potential ecological effects of the ejectors plant. Sediment characteristics, benthic, and fish assemblages before and after the plant activation have been analyzed in the putatively impacted (the sediment removal and discharge) areas and four control locations, one time before and two times after plant activation. Ejectors plant operation resulted in a reduction of the mud and organic matter content in the sediment, as well as in changes in shell debris amount in the impacted areas. Abundance and species richness of benthic macroinvertebrates, initially reduced in the impacted areas, probably due to the previous repeated dredging, returned to higher values during demo plant continuous operation. Higher diversity of fish fauna was observed in the study area during plant operation period. Observed dynamics of the ecological status of the marine habitat suggest that an ejectors plant could represent an eco-friendly solution alternative to dredging operations to solve harbor siltation problems.