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The Kootenai River ecosystem (spelled Kootenay in Canada) has experienced numerous ecological changes since the early 1900s. Some of the largest impacts to habitat, biological communities, and ecological function resulted from levee construction along the 120 km of river upstream from Kootenay Lake, completed by the 1950s, and the construction and operation of Libby Dam on the river near Libby Montana, completed in 1972. Levee construction isolated tens of thousands of hectares of historic functioning floodplain habitat from the river channel downstream in Idaho and British Columbia (B.C.) severely reducing natural biological productivity and habitat diversity crucial to large river-floodplain ecosystem function. Libby Dam greatly reduces sediment and nutrient transport to downstream river reaches, and dam operations cause large changes in the timing, duration, and magnitude of river flows. These and other changes have contributed to the ecological collapse of the post-development Kootenai River ecosystem and its native biological communities. In response to large scale loss of nutrients, experimental nutrient addition was initiated in the North Arm of Kootenay Lake in 1992, in the South Arm of Kootenay Lake in 2004, and in the Kootenai River at the Idaho-Montana border during 2005. This report characterizes baseline chlorophyll concentration and accrual (primary productivity) rates and diatom and algal community composition and ecological metrics in the Kootenai River for four years, one (2004) before, and three (2005 through 2007) after nutrient addition. The study area encompassed a 325 km river reach from the upper Kootenay River at Wardner, B.C. (river kilometer (rkm) 445) downstream through Montana and Idaho to Kootenay Lake in B.C. (rkm 120). Sampling reaches included an unimpounded reach furthest upstream and four reaches downstream from Libby Dam affected by impoundment: two in the canyon reach (one with and one without nutrient addition), a braided reach, and a meandering reach. The study design included 14 sampling sites: an upstream, unimpounded reference site (KR-14), four control (non-fertilized) canyon sites downstream from Libby Dam, but upstream from nutrient addition (KR-10 through KR-13), two treatment sites referred to collectively as the nutrient addition zone (KR-9 and KR-9.1, located at and 5 km downstream from the nutrient addition site), two braided reach sites (KR-6 and KR-7), and four meander reach sites (KR-1 through KR-4). A series of qualitative evaluations and quantitative analyses were used to assess baseline conditions and effects of experimental nutrient addition treatments on chlorophyll, primary productivity, and taxonomic composition and metric arrays for the diatom and green algae communities. Insufficient density in the samples precluded analyses of bluegreen algae taxa and metrics for pre- and post-nutrient addition periods. Chlorophyll a concentration (mg/m{sup 2}), chlorophyll accrual rate (mg/m{sup 2}/30d), total chlorophyll concentration (chlorophyll a and b) (mg/m{sup 2}), and total chlorophyll accrual rate (mg/m{sup 2}/30d) were calculated. Algal taxa were identified and grouped by taxonomic order as Cyanophyta (blue-greens), Chlorophyta (greens), Bacillariophyta (diatoms), Chrysophyta (goldens), and dominant species from each sample site were identified. Algal densities (number/ml) in periphyton samples were calculated for each sample site and sampling date. Principal Component Analysis (PCA) was performed to reduce the dimension of diatom and algae data and to determine which taxonomic groups and metrics were contributing significantly to the observed variation. PCA analyses were tabulated to indicate eigenvalues, proportion, and cumulative percent variation, as well as eigenvectors (loadings) for each of the components. Biplot graphic displays of PCA axes were also generated to characterize the pattern and structure of the underlying variation. Taxonomic data and a series of biological and ecological metrics were used with PCA for diatoms and algae. Algal metrics included a suite of abundance, diversity, richness, dominance, and other measures, whereas additional trophic status and chemical limnology metrics, Van Dam indices and morphological groupings were employed in diatom PCAs. Analysis of Variance (ANOVA) was carried out using chlorophyll metrics and taxa and metric arrays for the diatom and green algae community data for comparing site differences from 2004 through 2007. Clear, statistically significant, biological responses from chlorophyll metrics, and taxa and metrics of the diatom and algal communities were revealed following experimental nutrient addition in the Kootenai River. Chlorophyll metric responses were more often significant and generally greater in magnitude than diatom and green algae taxa and metric responses

Characterization of the Kootenai River Algae Community and Primary Productivity Before and After Experimental Nutrient Addition, 2004?2007 [Chapter 2, Kootenai River Algal Community Characterization, 2009 KTOI REPORT].