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The index of biotic integrity (IBI) is a commonly used measure of relative aquatic ecosystem condition; however, its application to coldwater rivers over large geographic areas has been limited. A seven-step process was used to construct and test an IBI applicable to fish assemblages in coldwater rivers throughout the U.S. portion of the Pacific Northwest. First, fish data from the region were compiled from previous studies and candidate metrics were selected. Second, reference conditions were estimated from historical reports and minimally disturbed reference sites in the region. Third, data from the upper Snake River basin were used to test metrics and develop the initial index. Fourth, candidate metrics were evaluated for their redundancy, variability, precision, and ability to reflect a wide range of conditions while distinguishing reference sites from disturbed sites. Fifth, the selected metrics were standardized by being scored continuously from 0 to 1 and then weighted as necessary to produce an IBI ranging from 0 to 100. The resulting index included 10 metrics: number of native coldwater species, number of age-classes of sculpins Cottus spp., percentage of sensitive native individuals, percentage of coldwater individuals, percentage of tolerant individuals, number of alien species, percentage of common carp Cyprinus carpio individuals, number of selected salmonid age-classes, catch per unit effort of coldwater individuals, and percentage of individuals with selected anomalies. Sixth, the IBI responses were tested with additional data sets from throughout the Pacific Northwest. Last, scores from two minimally disturbed reference rivers were evaluated for longitudinal gradients along the river continuum. The IBI responded to environmental disturbances and was spatially and temporally stable at over 150 sites in the Pacific Northwest. The results support its use across a large geographic area to describe the relative biological condition of coolwater and coldwater rivers with low species richness.

Since the early 2000s, biotic ligand models and related constructs have been a dominant paradigm for risk assessment of aqueous metals in the environment. We critically review 1) the evidence for the mechanistic approach underlying metal bioavailability models; 2) considerations for the use and refinement of bioavailability-based toxicity models; 3) considerations for the incorporation of metal bioavailability models into environmental quality standards; and 4) some consensus recommendations for developing or applying metal bioavailability models. We note that models developed to date have been particularly challenged to accurately incorporate pH effects because they are unique with multiple possible mechanisms. As such, we doubt it is ever appropriate to lump algae/plant and animal bioavailability models; however, it is often reasonable to lump bioavailability models for animals, although aquatic insects may be an exception. Other recommendations include that data generated for model development should consider equilibrium conditions in exposure designs, including food items in combined waterborne-dietary matched chronic exposures. Some potentially important toxicity-modifying factors are currently not represented in bioavailability models and have received insufficient attention in toxicity testing. Temperature is probably of foremost importance; phosphate is likely important in plant and algae models. Acclimation may result in predictions that err on the side of protection. Striking a balance between comprehensive, mechanistically sound models and simplified approaches is a challenge. If empirical bioavailability tools such as multiple-linear regression models and look-up tables are employed in criteria, they should always be informed qualitatively and quantitatively by mechanistic models. If bioavailability models are to be used in environmental regulation, ongoing support and availability for use of the models in the public domain are essential.

This paper presents a 30+ year record of changes in benthic macroinvertebrate communities and fish populations associated with improving water quality in mining-influenced streams. Panther Creek, a tributary to the Salmon River in central Idaho, USA suffered intensive damage from mining and milling operations at the Blackbird Mine that released copper (Cu), arsenic (As), and cobalt (Co) into tributaries. From the 1960s through the 1980s, no fish and few aquatic invertebrates could be found in 40 km of mine-affected reaches of Panther Creek downstream of the metals contaminated tributaries, Blackbird and Big Deer Creeks.Efforts to restore water quality began in 1995, and by 2002 Cu levels had been reduced by about 90%, with incremental declines since. Rainbow Trout (Oncorhynchus mykiss) were early colonizers, quickly expanding their range as areas became habitable when Cu concentrations dropped below about 3X the U.S. Environmental Protection Agency's biotic ligand model (BLM) based chronic aquatic life criterion. Anadromous Chinook Salmon (O. tshawytscha) and steelhead (O. mykiss) have also reoccupied Panther Creek. Full recovery of salmonid populations occurred within about 12-years after the onset of restoration efforts and about 4-years after the Cu chronic criteria had mostly been met, with recovery interpreted as similarity in densities, biomass, year class strength, and condition factors between reference sites and mining-influenced sites. Shorthead Sculpin (Cottus confusus) were slower than salmonids to disperse and colonize. While benthic macroinvertebrate biomass has increased, species richness has plateaued at about 70 to 90% of reference despite the Cu criterion having been met for several years. Different invertebrate taxa had distinctly different recovery trajectories. Among the slowest taxa to recover were Ephemerella, Cinygmula and Rhithrogena mayflies, Enchytraeidae oligochaetes, and Heterlimnius aquatic beetles. Potential reasons for the failure of some invertebrate taxa to recover include competition, and high sensitivity to Co and Cu.