Aquatic ecosystem assessment is a rapidly developing field, and one of the newer approaches to assessing the condition of rivers and lakes is the Reference Condition Approach. This is a significant advancement in biomonitoring because it solves the problem of trying to locate nearby control or reference sites when studying an ecosystem that may be degraded, a problem that bedevils traditional approaches. Rather than using upstream reference sites in a river system or next-bay-over reference sites in a lake, an array of ecologically similar, least-exposed to stress sites scattered throughout a catchment or region is used. Once the reference condition has been established, any site suspected of being impacted can be assessed by comparison to the reference sites, and its status determined. The Reference Condition database, once formed, can be used repeatedly. The Reference Condition is established by standardized sampling of both the biota and its environment at a number of reference sites. A variety of environmental variables is measured in conjunction with sampling the biota (usually benthic invertebrates). In this book, we describe the basic methods involved in selecting and sampling appropriate reference sites, comparing test sites to appropriate reference sites using predictive modeling, and determining whether or not test sites are in the reference condition. This provides a rapid assessment method that can deal with everything from large-scale, national issues to local-scale problems with the same approach, and often parts of the same database.