Multi-metric indices (MMIs) are a measure of a combination of characteristics of biological communities and are used as indicators of water quality and ecological health. Although MMIs for algal communities have been developed for specific regions of the United States, none of the indices have national applicability. The MMIs described in this report were developed by the National Water-Quality Assessment Program of the U.S. Geological Survey to assess the overall health of benthic algal communities in U.S. streams and rivers within five geographic regions that encompass the conterminous United States.The traditional procedure for developing MMIs (also referred to as indices of biological integrity) is to select individual metrics that, separately, can distinguish between undisturbed sites (selected for this study as reference sites) and predetermined disturbed sites. The metrics are then combined into a single index. In addition to traditional approaches for selecting individual metrics, the current study used stepwise logistic regressions to select sets of metrics that best predicted whether sites were in an undisturbed or a disturbed condition. Multi-metric indices and logistic regression models were developed for five regions of the United States using calibration datasets and were evaluated using independent validation datasets.