Delving in the Deep—Dominance of Non‐Native Species in Benthic Fish Assemblages in the Fragmented Large River Ecosystem of the Austrian Danube

River fragmentation through channelization and the construction of dams has strongly altered river ecosystems, leading to declines in native fish species and the proliferation of non‐natives. Knowledge gaps still exist about the effects of fragmentation on the structure of ecological assemblages throughout all habitats in large, fragmented rivers. We aimed to assess the impacts of impoundments on benthic fish assemblages in the Austrian Danube by comparing deep, offshore mid‐channel habitats of impounded and free‐flowing sections, examining seasonal differences, and assessing the use of deep and sheltered habitats connected to fast‐flowing mid‐channel habitats. Mid‐channel habitats of two slow‐flowing impoundments, their fast‐flowing head of the impoundment sections, and a free‐flowing section were sampled seasonally using an electrified benthic trawl. Fragmentation through damming changed the Austrian Danube and created slow and deep impoundments with little habitat variation that are dominated by non‐native goby species, comprising 80%–90% of relative abundance. The most dominant species was the racer goby ( Babka gymnotrachelus ), formerly considered infrequent in mid‐channel habitats of the Danube. Densities of native rheophilic species were generally low (< 3 individuals/100 m), but relative abundances were less skewed towards non‐native species in fast‐flowing sections. Unexpectedly high numbers of juveniles of protected percid species endemic to the Danube River Basin were encountered throughout all river sections, especially in slow‐flowing areas. Seasons did not show clear effects on the composition of benthic fish assemblages; however, all habitats were used by fish throughout the year, and deep and sheltered habitats were particularly used as wintering habitats. The results of this study reveal clear impacts of damming on benthic fish assemblages in previously underrepresented offshore habitats in a large, fragmented river. The inclusion of riverine offshore habitats in the ecological assessment of large rivers is paramount to collect comprehensive data from all parts of riverine ecosystems which can inform effective management strategies, such as habitat restoration. Bottom trawl surveys contribute to a comprehensive understanding of how riverine offshore habitats are used by fish, ensuring a complete picture of habitat use.