Functional and oxygenated stream beds provide crucial habitat for multiple endangered stream taxa, including endangered freshwater mussels, fishes, and insect larvae. Stream bed restoration measures such as substrate raking are often applied to mitigate excess fine sediment introductions and stream bed colmation, yet such measures are controversial. In this study, we conducted a systematic experiment in which sites with stream bed raking and removal of macrophytes were monitored over two years and compared with before-treatment conditions and untreated reference sites in the Swedish Brånsån stream, which still contains a population of the endangered freshwater pearl mussel Margaritifera margaritifera. The stream bed restoration resulted in improved habitat quality, as evident from decreased substrate compaction, increased redox potential, and oxygen supply into the stream bed. In contrast to previous studies in Central European catchments with more intensive agricultural catchment uses, the effects of the restoration measure were much longer, extending over two years. Consequently, stream bed raking and macrophyte removal can be considered a useful and more long-lasting restoration measure than currently assumed, especially in streams where excess input of fine sediment has already been mitigated, where catchment land use is rather extensive, and where near-natural flow regimes still prevail.