Maintenance and restoration of the biological integrity of aquatic ecosystems are key goals of the US Clean Water Act and related environmental regulations. Protocols for assessing biological integrity depend on taxonomic identifications, but taxonomic methods based on morphology have proven time-consuming and, at least for some taxa, imprecise. We hypothesized that integration of DNA barcodes (cytochrome oxidase I sequences) into bioassessment protocols would provide greater discriminatory ability and repeatability of taxonomic identifications at comparable time and cost.. Our research goals were to (1) build a library of DNA barcodes for Ephemeroptera, Plecoptera and Trichoptera (EPT) in Maryland and (2) compare the repeatability, taxonomic precision, and cost of EPT identifications based on morphology and DNA barcodes.  Analysis of larval DNAs from Maryland's bioassessment program revealed approximately twice as many operational taxonomic units (OTUs) as morphologically identified genera.  As yet, not all OTUs have been identified to species, but ongoing efforts to barcode adult specimens from museum collections and light trap surveys will help bring names to unidentified OTUs.  Surprisingly, comparison of repeat identifications among two DNA barcoding labs and two morphological taxonomy labs revealed similar levels of accuracy, with most DNA barcoding errors arising from processing errors and sample contamination.