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Humans affect ecosystems in many ways, and scientific field studies are no exception. If data collection disrupts environments or biota too much, it can lead to inaccurate conclusions in the study of interest or in subsequent studies. We evaluated whether stream electrofishing surveys could measurably disturb the benthic biofilms in two forested headwaters in western Oregon, USA. While the consequences of electrofishing to macroinvertebrates and fish have been assessed, to date no studies have quantified its influence on benthic biofilms. We observed declines in the standing stocks of accrued benthic chlorophylladirectly after electrofishing in both streams. After electrofishing, the standing biofilm stocks declined by an average of ~15% in Oak Creek, a small third‐order stream in the Oregon Coast Range Mountains, and by an average of ~34% in a third‐order section of Lookout Creek, which is located in the western Cascade Mountains of Oregon, USA. In returning to Oak Creek 2 weeks after electrofishing, the standing stocks had fully recovered to their prefishing levels. While the benthic biofilm standing stocks did decline in association with electrofishing, the effects were small when compared with those of disturbances from common flow events and when scaling to the whole stream system. In Oak Creek, the proportional biofilm standing stock decline from electrofishing activity was about 26% of what was observed following a moderate flow event (40% of bank‐full discharge), and about 15% of the decline in biofilm standing stocks following a complete bank‐full discharge event (140% of bank‐full discharge).