The Montana Department of Environmental Quality (MDEQ) recently developed two indicators of stream quality based on benthic macroinvertebrates.  The Multi-Metric Index (MMI) uses combined metric signals within three distinct site classes: Mountains, Low Valleys, and Plains.  The Observed/Expected (O/E) index quantifies taxa loss based on individual site potential.  We expected the two indicators to respond somewhat differently because they assess different aspects of biological conditions, and they showed contradictory results (inferred impaired vs. nonimpaired) in 29% of a random subset of sites.  We sought to understand why these differences occurred and explore if their different signals could be jointly interpreted to yield a combined impairment determination.  Correlation analysis and classification and regression trees showed that both collection method and natural environmental factors produced systematic errors in the values of both indicators.  These systematic errors might be reduced through future index refinements by incorporating additional reference site data.  In the interim, MDEQ can continue to use the two indicators by adjusting for these biases and then jointly interpreting their values.  For example, a combined threshold of impairment could be applied in cases where the MMI and O/E do not agree on impairment status.