A survey of the macrozoobenthos communities in the Maritsa River (South Bulgaria) was carried out in the summer of 2021. Benthic samples were collected and physicochemical parameters (water temperature, pH, conductivity, dissolved oxygen and nutrients) were measured at 15 sites located on the main river and its tributary system. The studied sites belonged to different river types and characterised the diversity of the ecological conditions—from unaffected to anthropogenically influenced river stretches. In addition, data from a study conducted in the summer of 2020 were used to analyse species–factor interactions in the river ecosystems and to assess the bio-indicative potential of the aquatic invertebrates. The dynamics of the taxonomic composition and abundance of the macrozoobenthos were analysed in relation to environmental factors. The physicochemical conditions of the water environment changed during the period of high water, which led to a reduction in the composition of the macrozoobenthos. Plecoptera and Trichoptera decreased in richness and abundance downstream and under human impacts. Ephemeroptera and Chironomidae were permanently present along the whole river. Oligochaeta increased in the lower river reaches and at sites with a greater amount of organic matter. The ecological status determined by the macrozoobenthos varied from high (site 1) to good, moderate and bad (site 13) at the studied sites.