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Abstract Leaf breakdown is an important process in forested headwater streams. A common method used to quantify the role of macroinvertebrate and microbial communities in leaf litter breakdown involves using paired mesh bags that either allow or exclude macroinvertebrate access to leaves. We examined common assumptions of the paired litterbag method to test (1) whether mesh size alters microbial respiration and (2) whether the effects of abrasive flows (e.g., from water and sediment) differ between coarse‐ and fine‐mesh litterbags. We measured rates of microbial respiration on Acer rubrum and Rhododendron maximum leaves incubated in coarse‐ and fine‐mesh litterbags. We also measured rates of abrasion using aerated concrete blocks in pairs of coarse‐ and fine‐mesh bags in ten streams across a gradient of discharge. We found that rates of microbial respiration on Acer rubrum leaves conditioned in fine‐mesh bags were 65% greater than the rates of respiration in paired coarse‐mesh bags, but respiration rates on Rhododendron maximum were similar in coarse‐ and fine‐mesh bags. Abrasion was, on average, 56% greater in coarse‐mesh than paired fine‐mesh bags, and these effects were greater in streams with higher discharge. These results suggest that more caution is required when attributing the difference in leaf breakdown between coarse‐ and fine‐mesh bags to macroinvertebrates. Because the effect of mesh size on microbial respiration of Acer leaves and abrasion are opposite in direction, the effect that dominates and creates bias likely depends on both environmental context and experimental design.