Reduction of flow constitutes one of the most severe human alterations to rivers, as it affects the key abiotic feature of these ecosystems. While there has been considerable progress in understanding the effects of reduced flow on benthic macroinvertebrates, cascading effects of flow reduction on dissolved oxygen concentrations (DO) have not yet received much attention. We compared the macroinvertebrate composition between reference conditions and a situation after several years of discharge reduction in the Spree River (Brandenburg, Germany). Community composition shifted from rheophilic species to species indifferent to flow conditions. Filter feeders were partially replaced by collector/gatherers, which likely reduces the retention of organic matter, and thus the self-purification capacity of the river section. These shifts were associated with low discharge during summer, cascading into daily DO concentration minima of less than 5 mg l−1 which prevailed 74% of the days in summer. This depletion of DO after flow reduction presumably caused the observed species turnover. Hence, flow reduction in lowland rivers may not only directly impair the ecological functions provided by benthic macroinvertebrates but may also act indirectly by depleting DO concentrations.