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The Upper Clark Fork River (UCFR) Long Term Research in Environmental Biology (LTREB) umbrella monitoring project generating these data is conducted separately and complementarily to the 200-million-dollar (USD) superfund project for ecological restoration of the UCFR, associated tributaries, and head water streams including Silver Bow and Warm Springs Creeks. Restoration along the UCFR in western Montana includes removal of metal-laden floodplain soils, lowering of the floodplain to its original elevation, and re-vegetation of over 70 km of the river’s floodplain closest to contaminant sources. The UCFR LTREB project includes bi-weekly water quality monitoring across the first 200 km of the river and its major tributaries along a gradient of heavy metal contamination associated with historic mining. Monitoring includes inorganic phosphorus and nitrogen concentrations, biotic standing stocks, and dissolved and whole-water heavy metal concentrations. The monitoring program began in 2017 with funding likely to be extended through 2028. The original analytical intent for these data was to assess the response of river dissolved organic carbon to the floodplain restoration. Data are multispectral absorbance and fluorescence analyses of organic carbon dissolved in samples of well-mixed river thalweg water. Data include excitation-emission matrices, absorbance spectroscopy, as well as absorbance and fluorometric summary indices calculated at specific wavelengths of excitation and emission. Data are from the 2019 water year (1 Oct 2018 to 30 Sep 2019). Data were collected on the Upper Clark Fork River (USGS HUC 17010201) at 13 project sites distributed along the river from the vicinity of Anaconda to Missoula, Montana, USA. 

The Upper Clark Fork River (UCFR) Long Term Research in Environmental Biology (LTREB) umbrella monitoring project generating these data is conducted separately and complementarily to the 200-million-dollar (USD) superfund project for ecological restoration of the UCFR, associated tributaries, and head water streams including Silver Bow and Warm Springs Creeks. Restoration along the UCFR in western Montana includes removal of metal-laden floodplain soils, lowering of the floodplain to its original elevation, and re-vegetation of over 70 km of the river’s floodplain closest to contaminant sources. The UCFR LTREB project includes bi-weekly water quality monitoring across the first 200 km of the river and its major tributaries along a gradient of heavy metal contamination associated with historic mining. Monitoring includes inorganic phosphorus and nitrogen concentrations, biotic standing stocks, and dissolved and whole-water heavy metal concentrations. The monitoring program began in 2017 with funding extended through 2028. The original analytical intent for these data was to assess the response of river dissolved organic carbon to the floodplain restoration. Data are Aurora Total Organic Carbon combustion analyses of the concentration of organic carbon dissolved in filtered samples of well-mixed river thalweg water. Data are from the 2021 water year (1 Oct 2020 to 30 Sep 2021) from samples collected on the Upper Clark Fork River (USGS HUC 17010201) at project sites distributed along the river from the vicinity of Anaconda to Missoula, Montana, USA. 

The Upper Clark Fork River (UCFR) Long Term Research in Environmental Biology (LTREB) umbrella monitoring project generating these data is conducted separately and complementarily to the 200-million-dollar (USD) superfund project for ecological restoration of the UCFR, associated tributaries, and head water streams including Silver Bow and Warm Springs Creeks. Restoration along the UCFR in western Montana includes removal of metal-laden floodplain soils, lowering of the floodplain to its original elevation, and re-vegetation of over 70 km of the river’s floodplain closest to contaminant sources. The UCFR LTREB project includes bi-weekly water quality monitoring across the first 200 km of the river and its major tributaries along a gradient of heavy metal contamination associated with historic mining. Monitoring includes inorganic phosphorus and nitrogen concentrations, biotic standing stocks, and dissolved and whole-water heavy metal concentrations. The monitoring program began in 2017 with funding extended through 2028. The original analytical intent for these data was to assess the response of river dissolved organic carbon to the floodplain restoration. Data are total organic carbon combustion analyses (Shimadzu Scientific Instruments) of the concentration of organic carbon dissolved in filtered samples of well-mixed river thalweg water. Data are from the 2024 water year (1 Oct 2023 to 30 Sep 2024) from samples collected on the Upper Clark Fork River (USGS HUC 17010201) at project sites distributed along the river from the vicinity of Anaconda to Missoula, Montana, USA. 

The Upper Clark Fork River (UCFR) Long Term Research in Environmental Biology (LTREB) umbrella monitoring project generating these data is conducted separately and complementarily to the 200-million-dollar (USD) superfund project for ecological restoration of the UCFR, associated tributaries, and head water streams including Silver Bow and Warm Springs Creeks. Restoration along the UCFR in western Montana includes removal of metal-laden floodplain soils, lowering of the floodplain to its original elevation, and re-vegetation of over 70 km of the river’s floodplain closest to contaminant sources. The UCFR LTREB project includes bi-weekly water quality monitoring across the first 200 km of the river and its major tributaries along a gradient of heavy metal contamination associated with historic mining. Monitoring includes inorganic phosphorus and nitrogen concentrations, biotic standing stocks, and dissolved and whole-water heavy metal concentrations. The monitoring program began in 2017 with funding extended through 2028. The original analytical intent for these data was to assess the response of river dissolved organic carbon to the floodplain restoration. Data are primarily Aurora Total Organic Carbon combustion analyses of the concentration of organic carbon dissolved in filtered samples of well-mixed river thalweg water. A few samples from the final campaign in the dataset were analyzed with a Shimadzu instrument using a similar method. Data are from the 2022 water year (1 Oct 2021 to 30 Sep 2022) from samples collected on the Upper Clark Fork River (USGS HUC 17010201) at project sites distributed along the river from the vicinity of Anaconda to Missoula, Montana, USA. 

The Upper Clark Fork River (UCFR) Long Term Research in Environmental Biology (LTREB) umbrella monitoring project generating these data is conducted separately and complementarily to the 200-million-dollar (USD) superfund project for ecological restoration of the UCFR, associated tributaries, and head water streams including Silver Bow and Warm Springs Creeks. Restoration along the UCFR in western Montana includes removal of metal-laden floodplain soils, lowering of the floodplain to its original elevation, and re-vegetation of over 70 km of the river’s floodplain closest to contaminant sources. The UCFR LTREB project includes bi-weekly water quality monitoring across the first 200 km of the river and its major tributaries along a gradient of heavy metal contamination associated with historic mining. Monitoring includes inorganic phosphorus and nitrogen concentrations, biotic standing stocks, and dissolved and whole-water heavy metal concentrations. The monitoring program began in 2017 with funding extended through 2028. The original analytical intent for these data was to assess the response of river dissolved organic carbon to the floodplain restoration. Data are total organic carbon combustion analyses (Shimadzu Scientific Instruments) of the concentration of organic carbon dissolved in filtered samples of well-mixed river thalweg water. Data are from the 2023 water year (1 Oct 2022 to 30 Sep 2023) from samples collected on the Upper Clark Fork River (USGS HUC 17010201) at project sites distributed along the river from the vicinity of Anaconda to Missoula, Montana, USA. 

Abstract Rivers efficiently collect, process, and transport terrestrial‐derived carbon. River ecosystem metabolism is the primary mechanism for processing carbon. Diel cycles of dissolved oxygen (DO) have been used for decades to infer river ecosystem metabolic rates, which are routinely used to predict metabolism of carbon dioxide (CO₂) with uncertainties of the assumed stoichiometry ranging by a factor of 4. Dissolved inorganic carbon (DIC) has been less used to directly infer metabolism because it is more difficult to quantify, involves the complexity of inorganic carbon speciation, and as shown in this study, likely requires a two‐station approach. Here, we developed DIC metabolism models using single‐ and two‐station approaches. We compared metabolism estimates based on simultaneous DO and DIC monitoring in the Upper Clark Fork River (USA), which also allowed us to estimate ecosystem‐level photosynthetic and respiratory quotients (PQ_Eand RQ_E). We observed that metabolism estimates from DIC varied more between single‐ and two‐station approaches than estimates from DO. Due to carbonate buffering, CO₂is slower to equilibrate with the atmosphere compared to DO, likely incorporating a longer distance of upstream heterogeneity. Reach‐averaged PQ_Eranged from 1.5 to 2.0, while RQ_Eranged from 0.8 to 1.5. Gross primary production from DO was larger than that from DIC, as was net ecosystem production by . The river was autotrophic based on DO but heterotrophic based on DIC, complicating our understanding of how metabolism regulated CO₂production. We suggest future studies simultaneously model metabolism from DO and DIC to understand carbon processing in rivers. 

Abstract The Upper Clark Fork River (UCFR), Montana, a mid-order well-lit system with contemporary anthropogenic nitrogen (N) enrichment and natural geogenic sources of phosphorus (P), experiences annual algal blooms that influence ecosystem structure and function. This study was designed to assess the occurrence of riverine algal blooms (RABs) in the UCFR by characterizing the succession of periphyton and biogeochemical conditions following annual snowmelt runoff through autumnal baseflow conditions, and to provide a framework for assessing RAB progression in montane mid-order rivers more broadly. Using a 21-year database (2000–2020) collected over the growing season at three sites, historical assessment of the persistent and recurrent character of RABs in the UCFR showed that the magnitude of the summer bloom was, in part, moderated by snowmelt disturbance. Abundance and growth forms of benthic algae, along with river physicochemistry (e.g., temperature) and water chemistry (N and P concentration), were measured over the course of snowmelt recession for three years (2018–2020) at the same three sites. Results documented the onset of major blooms of the filamentous green algaeCladophoraacross all sites, commensurate with declines in dissolved inorganic N. Atomic N:P ratios of river water suggest successional transitions from P- to N-limitation associated with mid-season senescence ofCladophoraand development of a secondary bloom of N-fixing cyanobacteria, dominated byNostoc cf. pruniforme. Rates of N-fixation, addressed at one of the sites during the 2020 snowmelt recession, increased uponCladophorasenescence to a maximal value among the highest reported for lotic systems (5.80 mg N/m²/h) before decreasing again to background levels at the end of the growing season. Based on these data, a heuristic model for mid-order rivers responding to snowmelt disturbance suggests progression from phases of physical stress (snowmelt) to optimal growth conditions, to conditions of biotic stress later in the growing season. Optimal growth is observed as green algal blooms that form shortly after peak snowmelt, then transition to stages dominated by cyanobacteria and autochthonous N production later in the growing season. Accordingly, interactions among algal composition, reactive N abundance, and autochthonous N production, suggest successional progression from reliance on external nutrient sources to increased importance of autochthony, including N-fixation that sustains riverine productivity during late stages of snowmelt recession. 

Harmful and nuisance algal blooms are becoming a greater concern to public health, riverine ecosystems, and recreational uses of inland waterways. Algal bloom proliferation has increased in the Upper Clark Fork River due to a combination of warming water temperatures, naturally high phosphorus levels, and an influx of nitrogen from various sources. To improve understanding of bloom dynamics and how they affect water quality, often measured as algal biomass measured through pigment standing crops, a UAV-based hyperspectral imaging system was deployed to monitor several locations along the Upper Clark Fork River in western Montana. Image data were collected across the spectral range of 400–1000 nm with 2.1 nm spectral resolution during two field sampling campaigns in 2021. Included are methods to estimate chl a and phycocyanin standing crops using regression analysis of salient wavelength bands, before and after separating the pigments according to their growth form. Estimates of chl a and phycocyanin standing crops generated through a linear regression analysis are compared to in situ data, resulting in a maximum R2 of 0.96 for estimating fila/epip chl-a and 0.94 when estimating epiphytic phycocyanin. Estimates of pigment standing crops from total abundance, epiphytic, and the sum of filamentous and epiphytic sources are also included, resulting in a promising method for remotely estimating algal standing crops. This method addresses the shortcomings of current monitoring techniques, which are limited in spatial and temporal scale, by proposing a method for rapid collection of high-spatial-resolution pigment abundance estimates.