Difficulty in diatom species identification and nomenclature can lead to major inconsistencies in taxonomic datasets. These inconsistencies may hinder the use of diatoms in large-extent bioassessments such as the U.S. Environmental Protection Agency’s (U.S. EPA) National Aquatic Resource Surveys. We addressed this problem by developing diatom multimetric indices (MMIs) of ecological condition using genus-level taxonomy and trait-based information (e.g., tube-living, motile and/or nitrogen-fixing diatoms) collected from the 2008-09 U.S. EPA National Rivers and Stream Assessment (NRSA). The MMIs were designed to assess ecological condition for >3,000 rivers and streams across the U.S. Genus-level, trait-based indices have the advantage over traditional species-based indices of using genus-level data which require less work-effort and expertise and therefore are less costly to analyze. Using genus-level taxonomy also eliminates the persistent taxonomic biases introduced over vast geographic extents because genus-level identifications are less prone to taxonomic errors, thus improving the taxonomic consistency and quality of large datasets involving multiple analysts. The genus-level trait MMIs responded well to increases in multiple stressors; discriminating least-disturbed from most-disturbed sites. This new indicator will allow for the use of diatoms in future NRSA surveys. Similar genus-level MMIs are also being developed for use in the U.S. EPA’s National Wetland Condition Assessment. Our genus-based approach can be effective for spatially extensive assessments and facilitates including of diatoms into assessment programs that have limited monitoring resources.