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Benthic invertebrates are used by a number of agencies worldwide as indicators for assessing stream health, which has resulted in the development of a variety of protocols for collecting and processing benthic samples. The large number of methods used means that calibration of data collection is not always possible, but if different methods produce similar estimates of community composition and metric values, then sharing of data can make bioassessments more efficient. This study explored the effect of two approaches to subsampling and sorting of benthic invertebrates on community composition, calculation of metrics, and assessment of stream health. We compared two commonly used sampling methods: a rapid approach, employing live, unaided sorting and a standard approach using microscope sorting of preserved samples, through a comparison of replicate samples collected from 61 streams. This study found that both methods resulted in similar estimates of community composition at a site, as determined by the Bray-Curtis similarity index. However, the live sorting methodology resulted in greater family richness and higher estimates of metrics that reflect large taxa (i.e., %EPT). Despite differences in a number of metrics, both methods performed equally well at identifying impairment in the test sites, with livesorting samples slightly more sensitive.