The objectives of the Environmental Monitoring and Assessment Program for Great River Ecosystems (EMAP-GRE) are to (1) develop and demonstrate, in collaboration with states, an assessment program yielding spatially unbiased estimates of the condition of mid-continent great rivers; (2) evaluate environmental indicators for assessing great rivers; and (3) assess the current condition of selected great river resources. The purpose of this paper is to describe EMAP-GRE using examples based on data collected in 2004-2006 with emphasis on an approach to determining reference conditions. EMAP-GRE includes the Upper Mississippi River, the Missouri River, and the Ohio River. Indicators include biotic assemblages (fish, macroinvertebrates, plankton, algae), water chemistry, and aquatic and riparian physical habitat. Reference strata (river reaches for which a single reference expectation is appropriate) were determined by ordination of the fish assemblage and examination of spatial variation in environmental variables. Least disturbed condition of fish assemblages for reference strata was determined by empirical modeling in which we related fish assemblage metrics to a multimetric stressor gradient. We inferred least disturbed condition from the y-intercept, the predicted condition when stress was least. Thresholds for dividing the resource into management-relevant condition classes for biotic indicators were derived using predicted least disturbed condition to set the upper bound on the least disturbed condition class. Also discussed are the outputs of EMAP-GRE, including the assessment document, multimetric indices of condition, and unbiased data supporting state and tribal Clean Water Act reporting, adaptive management, and river restoration.

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The persistence of plankton in flowing water presents an enigma, i.e., how can populations be sustained while constantly losing individuals downriver? We examined the distribution and abundance of zooplankton from 146 sites on the Missouri River (USA) and found large shifts in the dominance of major taxa between management zones of this regulated river. Crustacean zooplankton were dominant in the inter-reservoir zone of the river, and their taxonomic composition was similar to regional lakes and reservoirs. The exponential decline of cladocerans and copepods with distance from main-stem dams suggests that conditions within the river are adverse to population growth and that reservoirs are the main source of these crustaceans in the river. Rotifers dominated in the channelized zone of the river. High algal biomass and rapid population growth rates likely allow persistence of rotifers in segments of the river that do not receive direct reservoir inputs. Rotifers were less abundant in the inter-reservoir zone, suggesting that their numbers are limited by internal processes, such as food or predators. Since zooplankton are known to be an important food for larval fishes in rivers, this shift of major taxa in regulated rivers has implications for river food webs.

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The hypothesis that economic damage due to nonpoint pollution exceeds costs of mitigation can he tested by ecologists, economists, and resource managers working at the spatial scale of watersheds for periods of years to decades. We present a framework for combining ecological and economic information to compare management scenarios for nonpoint pollution. Eutrophication of lakes caused by nonpoint phosphorus pollution, a common environmental problem, is the focus of our approach. Economic advantages of mitigating nonpoint pollution increase as the uncertainty of ecological predictions decreases. Uncertainty is measured by the prediction variance of nonpoint pollution models. A major source of variance in nonpoint pollution predictions is the effect of land use change on phosphorus transport. This variance is often large because calibration data sets do not have sufficiently wide ranges of land use variables. Ecological predictions and the resulting economic assessments could be improved by comparative studies of watersheds with contrasting land uses, and by viewing nonpoint pollution management as a largescale experiment.