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Forestry-related land use can cause increasing instream sedimentation, burying and eradicating stream bryophytes, with severe ecological consequences. However, there is limited understanding of the relative roles and overall importance of the two frequently co-occurring stressors, increased fine sediments and loss of bryophytes, to stream biodiversity and ecosystem functions. By using random forest modeling and partial dependence functions, we studied the relative importance of stream bryophytes and fine sediments to multiple biological endpoints (leaf-decaying fungi, diatom, bryophyte, and benthic macroinvertebrate communities; leaf decomposition) using field survey data from headwater streams. Stream bryophyte abundance and richness were negatively related to fine sediment cover, highlighting the detrimental effect of sedimentation on bryophytes. However, bryophyte abundance was consistently more important a determinant of variation in community composition than was fine sediment cover. Leaf decomposition was influenced by shredder abundance, water temperature and, to a lesser degree, stream size. Our results suggest that the loss of stream bryophytes due to increasing sedimentation, rather than fine sediments per se, seems to be the key factor affecting multiple biological responses. Enhancing the re-establishment of bryophyte stands could partly compensate for the negative impacts of sedimentation on bryophytes and, consequently, on several other components of boreal stream ecosystems.