An important component of the biological assessment of stream condition is an evaluation of the direct or indirect effects of human activities or disturbances. The concept of a "reference condition" is increasingly used to describe the standard or benchmark against which current condition is compared. Many individual nations, and the European Union as a whole, have codified the concept of reference condition in legislation aimed at protecting and improving the ecological condition of streams. However, the phrase "reference condition" has many meanings in a variety of contexts. One of the primary purposes of this paper is to bring some consistency to the use of the term. We argue the need for a "reference condition" term that is reserved for referring to the "naturalness" of the biota (structure and function) and that naturalness implies the absence of significant human disturbance or alteration. To avoid the confusion that arises when alternative definitions of reference condition are used, we propose that the original concept of reference condition be preserved in this modified form of the term: "reference condition for biological integrity," or RC(BI). We further urge that these specific terms be used to refer to the concepts and methods used in individual bioassessments to characterize the expected condition to which current conditions are compared: "minimally disturbed condition" (MDC); "historical condition" (HC); "least disturbed condition" (LDC); and "best attainable condition" (BAC). We argue that each of these concepts can be narrowly defined, and each implies specific methods for estimating expectations. We also describe current methods by which these expectations are estimated including: the reference-site approach (condition at minimally or least-disturbed sites); best professional judgment; interpretation of historical condition; extrapolation of empirical models; and evaluation of ambient distributions. Because different assumptions about what constitutes reference condition will have important effects on the final classification of streams into condition classes, we urge that bioassessments be consistent in describing the definitions and methods used to set expectations.

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The ratio of the number of observed taxa to that expected to occur in the absence of human‐caused stress (O/E) is an intuitive and ecologically meaningful measure of biological integrity. We examined how O/E ratios derived from stream invertebrate data varied among 234 unimpaired reference sites and 254 test sites potentially impaired by past logging. Data were collected from streams in three montane ecoregions in California. Two sets of River Invertebrate Prediction and Classification System (RIVPACS) predictive models were built: one set of models was based on near‐species taxonomic resolution; the other was based on family identifications. Two models were built for each level of taxonomic resolution: one calculated O and E based on all taxa with probabilities of capture (Pc) > 0; the other calculated O and E based on only those taxa with Pc ≥ 0.5. Evaluations of the performance of each model were based on three criteria: (1) how well models predicted the taxa found at unimpaired sites, (2) the degree to which O/E values differed among unimpaired reference sites and potentially impaired test sites, and (3) the degree to which test site O/E values were correlated with independent measures of watershed alteration. Predictions of species models were more accurate than those of family models, and predictions of the Pc ≥ 0.5 species model were more robust than predictions of the Pc ≥ 0 model. O/E values derived from both species models were related to land use variables, but only assessments based on the Pc ≥ 0.5 model were insensitive to naturally occurring differences among streams, ecoregions, and years.

SUMMARY 1. We analysed an existing database of macroinvertebrates and fish in the context of a newly established geographical information system (GIS) of physical features to determine the relationships between stream community composition and physical factors measured at three landscape scales – catchment, reach and bedform. Both an exploratory (concordance analysis) and a predictive (ausrivas) approach were used. 2. The environmental variables that most successfully accounted for variation in macroinvertebrate assemblages were mainly ‘natural’ and at the catchment‐scale (relief ratio, basin diameter, etc.) but the human‐induced physical setting of percentage of pasture in the riparian zone was also influential. For fish, ‘natural’ variables were also dominant, but these were mostly at the bedform or reach scales and land use featured strongly. 3. Geographic location accounted for some of the variation in invertebrate assemblages, partly because geography and influential conditions/resources are correlated but also because different species may have evolved in different places and have not colonised every ‘ecologically appropriate’ location. Geographic location was not influential in accounting for variation in assemblages of strongly flying invertebrates, supporting the hypothesis that organisms having high dispersal potential can be expected to break down geographic barriers more readily than those with poor dispersal powers. In accord with what is known about the local evolution and restricted distributions of native and exotic species, history (reflected in geography) appeared to account for some variation in fish assemblages. 4. Given their different mathematical bases, the fact that exploratory and predictive analyses yielded similar results provides added confidence to our conclusions.

Benthic macroinvertebrates are the group of organisms most widely used for assessment of water resources. Rapid assessment approaches are intended to be efficient and cost effective; savings are found in reduced sampling and more efficient data analysis. Rapid bioassessment programmes have been quickly accepted and now cover most of the United States (US) and equivalent programmes cover all of the United Kingdom (UK). Rapid bioassessment programmes are designed to screen large regions, pinpointing trouble spots worthy of more detailed attention.Fundamental to all rapid bioassessment methods is the classification of streams so that comparisons can be made between reference areas and areas of concem, or test sites with similar characteristics. Both the UK and US approaches assess habitat characteristics. These characteristics are used to predict the fauna expected at a test site in the UK approach; in the US they are used as an aid to classification and interpretation of aquatic faunal data. Habitat assessments in the US are also used to determine whether poor water quality or degraded habitat are stressing the invertebrate communities. This is a major development in approaches to water resource assessment.In the UK, a model developed using multivariate statistics uses a few environmental variables thought to be unaffected by human activities to predict the fauna expected at a test site. The US approaches analyse data using several indices (or metrics) presumed to represent ecological features of interest. These indices have a range of sensitivities to different kinds of stress and must be calibrated for the area of interest. The two approaches have been developed in isolation but may have much to offer each other. Developing programmes are advised to consider both.Future needs include: development of procedures that can be applied to large rivers and to lakes; further refinement of ecological principles underlying metric choice; the inclusion of chemical criteria and toxicity tests to establish thresholds that indicate impairment; and development of criteria indicating the necessity for implementation of quantitative assessment studies.