This research examines the river mouth ecosystems of Kizilirmak and Yeşilirmak, discharging significant quantities of freshwater and nutrients to the Samsun Shelf area along the mid-southern Black Sea. The objective was to ascertain the current ecological status and detect any significant variation between two river mouth ecosystems (rehabilitated-Kizilirmak and natural-Yeşilırmak) in terms of macroinvertebrate communities and environmental variables. Sampling was conducted seasonally between February 2017 - November 2017. A total of 52206 individuals belonging to 90 taxa were identified. In Kızılırmak river mouth 51 species were identified and 60 species belonging to Yeşilırmak. All identified taxa are new records for the study area and Orthocladius (Orthocladius) dentifer, O. (O.) clarkei, O. (O.) dorenus, O. (O.) wetterenesis, O. (O.) mixtus and Mystacides longicornis were found to be new records for the macrobenthic fauna of Turkey. The distribution of macroinvertebrates was compared by means of season, area, particle size, and station groups. It is found that Kızılırmak and Yeşilırmak river mouth ecosystems are represented by a narrow habitat fragment. In Kızılırmak river mouth habitat a high level of similarity among stations and a significant loss of diversity across the site was determined. This phenomenon is believed to be the natural outcome of reconstruction activities along the downstream resulting in ecosystem destruction. The Yeşilirmak river mouth habitat is determined to a have a relatively more diverse macrobenthic community and seemed to be well preserved than the Kızılırmak area.