The monitoring of aquatic communities is a common way to assess impacts of human activities in a watershed. However, aquatic communities can show substantial temporal variability as the result of natural processes. A well designed monitoring program is necessary in order to identify the difference between potential impacts and natural variation. The Thompson Creek Molybdenum Mine is located in the Thompson Creek and Squaw Creek watershed in central Idaho. The monitoring program for the mine

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... uded upstream reference sites, and the sampling of multiple organisms with quantitative techniques over many years. Fish and macroinvertebrate data have been collected for these streams upstream and downstream of the mine site since 1980, which includes the period prior to construction through operation to present. Using this long-term data set and the Idaho Department of Environmental Quality (IDEQ) Water Body Assessment Guidance Document, the natural variation at study sites upstream of any potential mining impacts was compared to the variation at study sites downstream of the mining activities. For macroinvertebrate data, the IDEQ index varied from very good to poor among the various years in Thompson and Squaw creeks. The range of variability was similar at upstream reference sites and sites downstream of the mine. This analysis points out the importance of monitoring both reference sites and potentially impacted sites for long periods of time. Changes in the macroinvertebrate community which might have been attributed to the mine were likely the result of natural variation.