@article {83165,
	title = {Oregon Water Quality Index Summary Report: Water Years 2013-2022},
	year = {2023},
	note = {Trends in water quality.  Raw data for earlier years is available in spreadsheet format.},
	month = {2023, Feb.},
	pages = {9 p.},
	institution = {Oregon Dept. of Environmental Quality. Laboratory and Environmental Assessment Division},
	address = {Hills boro, Or.},
	keywords = {agriculture, bacteria, dissolved oxygen, forestry, human impacts, land use, nitrogen, pH, phosphorus, water pollution, water quality, water temperature},
	url = {https://digital.osl.state.or.us/islandora/object/osl\%3A1008713},
	author = {Oregon Dept. of Environmental Quality,}
}
@article {37626,
	title = {Water Quality Index},
	year = {2022},
	note = {Trends in water quality. This website includes an interactive map and subbasin reports giving trends in recent years.},
	address = {Hillsboro, Or.},
	keywords = {bacteria, dissolved oxygen, nitrogen, pH, phosphorus, pollution, solids, water quality, water temperature},
	url = {https://www.oregon.gov/deq/wq/Pages/WQI.aspx},
	author = {Oregon. Dept. of Environmental Quality,}
}
@article {83124,
	title = {Understanding dissolved oxygen concentrations in a discontinuously perennial stream within a managed forest},
	journal = {Forest Ecology and Management},
	volume = {479},
	number = {118531},
	year = {2021},
	note = {The classic Alsea Watershed Study (1958-1973) established ways that traditional logging methods harmed aquatic organisms. Practices such as dumping slash in streams lowered the amount of dissolved oxygen available to fishes.  This paper gives data from a second (The Alsea Watershed Study Revisited, 2006-2015) look at the streams featured in the original Study, in light of contemporary forest management practices.  The new research shows that small streams that can go dry in times of low flow may naturally have periods of low oxygen unrelated to logging. Contemporary logging does not seem to affect dissolved oxygen levels in streams. },
	month = {2021, Jan. 1},
	pages = {14 p.},
	keywords = {Alsea River Basin, Alsea Watershed Study, Deer Creek, dissolved oxygen, Drift Creek, Flynn Creek, human impacts, logging, natural resource management, Needle Branch, riparian areas, terrestrial vegetation, water quality, water temperature},
	doi = {https://doi.org/10.1016/j.foreco.2020.118531},
	author = {Ice, George G. and Hale, V. Cody and Light, Jeffrey T. and Muldoon, Ariel and Simmons, Amy and Bousquet, Terry}
}
@mastersthesis {83154,
	title = {Ecosystem Functions of Pacific Northwest Estuaries: The Role of Ocean and Watershed Drivers in Eelgrass and Coho Salmon Dynamics},
	year = {2020},
	note = {This wide-ranging doctoral dissertation aims to {\textquotedblleft}investigate ocean and watershed dynamics to better understand the key drivers and consequences of ecosystem change in Pacific Northwest (PNW) estuaries{\textquotedblright} (from the Abstract). Topics explored include eelgrass and macroalgae, coho salmon and the Dungeness crab catch. },
	pages = {274 p.},
	school = {Oregon State University},
	type = {Doctoral Dissertation},
	edition = {Ph. D.},
	chapter = {Dept. of Integrative Biology},
	address = {Corvallis, Or.},
	keywords = {Alsea Bay, Beaver Creek, carbon dioxide, climate, Coho salmon = Oncorhynchus kisutch, Coos Bay, dissolved oxygen, Dungeness crab =   Metacarcinus magister (Cancer magister), eelgrass = Zostera marina, El Nino, Oregon Coast, Pacific Decadal Oscillation, pH, phosphate, precipitation, salinity, sea lettuce = Ulva spp., Siletz Bay, Siuslaw River estuary, Umpqua River, upwelling, water temperature, Yaquina Bay},
	url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/gt54kv37z },
	author = {Magel, Caitlin L.}
}
@article {54876,
	title = {Records of trace metals in sediments from the Oregon shelf and slope: Investigating the occurrence of hypoxia over the past several thousand years},
	journal = {Chemical Geology },
	volume = {382},
	year = {2014},
	note = {In recent years, strong coastal winds have caused strong upwelling events, so strong that a layer of low-oxygen seawater has been brought closer to the surface, leading to mass die-offs of marine life, and affecting estuarine waters as well.  A current question about these hypoxic events has to do with whether or not they are related to climate change.  A look at the history of the region is therefore called for.  {\textquotedblleft}A record of past hypoxia occurrence frequency would help distinguish human-induced causes from those related to natural climate changes. . . .  Determining trends in trace metal abundances can serve as an indicator for changes in oxygenation conditions over time.{\textquotedblright} (p.33) The authors look at trace metals in sediments from the Yaquina, Alsea and Siuslaw Rivers and consider other factors possibly influencing their data. {\textquotedblleft}Supplementary data to this article can be found online at http://dx.doi.org/10.1016/j.chemgeo.2014.05.029 .{\textquotedblright} (p.42)},
	month = {2014, Aug.29},
	pages = {p.32{\textendash}43},
	keywords = {Alsea Bay, chemistry, climate change, dissolved oxygen, hypoxia, paleosciences, sediments, Siuslaw Bay, Trace metals, winds, Yaquina Bay},
	doi = {10.1016/j.chemgeo.2014.05.029},
	author = {Erhardt, Andrea M. and Reimers, Clare E. and Kadko, David and Paytan, Adina}
}
@article {37031,
	title = {Oregon{\textquoteright}s 2012 Integrated Report},
	year = {2012},
	note = {Website includes:  an assessment database with information on water quality for waters in Oregon (includes water quality limited waters and 303(d) list waters), the assessment methodology used to evaluate data, and a schedule to develop TMDLs for waters identified in the Section 303(d) list.},
	keywords = {algae, bacteria, dissolved oxygen, general, habitats, pH data, sediments, water pollution, water quality, water temperature},
	url = {https://www.deq.state.or.us/wq/assessment/rpt2012/search.asp},
	author = {Oregon. Dept. of Environmental Quality,}
}
@inbook {51326,
	title = {Impacts of climate change on Oregon{\textquoteright}s coasts and estuaries},
	booktitle = {Oregon Climate Assessment Report},
	year = {2010},
	note = {This is Chapter 6 of the Oregon Climate Assessment Report. Predicts {\textquotedblleft}Increased winter{\textendash}early spring flow of coastal rivers and creeks and reduced flow during summer{\textquotedblright} for the Umpqua River (p.242)},
	pages = {p.211-268},
	publisher = {Oregon State University. College of Oceanic and Atmospheric Sciences. Oregon Climate Change Research Institute,},
	organization = {Oregon State University. College of Oceanic and Atmospheric Sciences. Oregon Climate Change Research Institute,},
	address = {Corvallis, Or.},
	keywords = {Alsea Bay, Alsea Spit, bacteria, Bayocean Spit, climate change, climate precipitation, coastal hazards, Columbia River estuary, Coos Bay, dissolved oxygen, El Nino, erosion, estuaries, geology, landslides, Nehalem Bay, Nehalem Spit, Neskowin (Or.), Netarts Bay, ocean acidification, Rockaway Beach, salinity, Salmon River Estuary, sea level, Siletz Bay, Tillamook Bay, water temperature, wave heights, Yachats River, Yaquina Bay},
	url = {https://digital.osl.state.or.us/islandora/object/osl\%3A637577},
	author = {Ruggiero, Peter and Brown, Cheryl A. and Komar, Paul D. and Allan, Jonathan C. and Reusser, Deborah A. and Lee II, Henry},
	editor = {Dello, Kathie and Mote, Philip W.}
}
@article {26816,
	title = {Oregon{\textquoteright}s 2010 Integrated Report},
	year = {2010},
	note = {Website includes:  an assessment database with information on water quality for waters in Oregon (includes water quality limited waters and 303(d) list waters), the assessment methodology used to evaluate data, and a schedule to develop TMDLs for waters identified in the Section 303(d) list.},
	keywords = {algae, bacteria, dissolved oxygen, general, habitats, pH data, sediments, water pollution, water quality, water temperature},
	url = {https://www.deq.state.or.us/wq/assessment/rpt2010/search.asp},
	author = {Oregon. Dept. of Environmental Quality,}
}
@article {83256,
	title = {Limiting Factors Assessment and Restoration Plan:  Middle and Upper Five Rivers, Tributary to the Alsea River},
	year = {2008},
	note = {{\textquotedblleft}This document provides watershed restoration actions proposed to enhance the coho salmon population within the Middle and Upper Fiver Rivers Sixth Field basins in Lincoln and Lane Counties, Oregon. . . The goal of the restoration effort has been to identify the dominant processes and habitat characteristics that limit the production of coho salmon smolts in the subbasins, and to develop a prioritized list of actions ({\textquotedblleft}prescriptions{\textquotedblright}) for removing the limitations in ways that normalize landscape and stream channel function{\textquotedblright} (from the Introduction).  Both summer and winter habitats needed improvement.  The area had gone from an historic average of 71 beaver dams to only 3 in 2007, so re-introducing American beaver was recommended.  Color photographs.},
	month = {2008, Apr.},
	pages = {91 p.},
	keywords = {agriculture, Alder Creek, American beaver = Castor canadensis, Cedar Creek, Coho salmon = Oncorhynchus kisutch, Crazy Creek, cutthroat trout = Oncorhynchus clarki, dissolved oxygen, Fendall Creek, fish passage, habitat restoration, habitats, human impacts, hydrology, marshes, Summers Creek, water quality, water temperature, Woosley Creek},
	url = {https://tinyurl.com/4e3fjsve },
	author = {Bio-Surveys LLC, and Holbert, Mary and Sialis Company,,}
}
@article {15546,
	title = {Ecological Condition of the Estuaries of Oregon and Washington},
	volume = {EPA-910-R-06-001},
	year = {2006},
	note = {For the layperson, this is an overview that does not go into any detail on specific estuaries. Problem locations are marked with colored dots on a map and are not labelled. This deliberate lack of specificity on EPA{\textquoteright}s part is baffling and disappointing.},
	pages = {73 p.},
	institution = {U.S. Environmental Protection Agency, Region 10, Office of Environmental Assessment},
	address = {Seattle, Wa.},
	keywords = {biodegradation, carbon, dissolved oxygen, ecosystem health, estuaries, heavy metals, hydrocarbons, invasive species, nitrogen, pesticides, phosphorus, sediments, species composition, species list, toxicity, water pollution, water quality},
	url = {https://archive.epa.gov/emap/archive-emap/web/pdf/cemapfinal.pdf},
	author = {U.S. Environmental Protection Agency. Region X, and U.S. Environmental Protection Agency. Region X. Office of Environmental Assessment,}
}
@article {15866,
	title = {NOAA{\textquoteright}s Estuarine Eutrophication Survey : Pacific Coast Region},
	volume = {5},
	year = {1998},
	note = {"In Alsea River, chlorophyll <i>a</i> concentrations are high in the seawater zone and turbidity concentrations are unknown. Nuisance or toxic bloom events are unknown, as are nitrogen and phosphorus concentrations. Anoxia, hypoxia and biological stress are not observed in this system. SAV [submerged aquatic vegetation] spatial coverage ranges from low to medium.  Dissolved oxygen observations and SAV spatial coverage have not changed. All other trends are unknown." (p.48)},
	month = {April_1998},
	pages = {75 p.},
	institution = {Office of Ocean Resources Conservation and Assessment},
	address = {Silver Spring, Md.},
	keywords = {algal species, Alsea River, aquatic vegetation, biological, Coos Bay, Coquille River, dissolved oxygen, hydrology, Nehalem River, Netarts Bay, nitrogen, phosphorus, physical, Rogue River, Siletz Bay, Siuslaw River, Tillamook Bay, toxicity, turbidity, Umpqua River, Yaquina Bay, Yaquina River},
	url = {https://archive.org/details/noaasestuarineeu00unit/mode/2up?ref=ol\&view=theater},
	author = {U.S. National Oceanic and Atmospheric Administration,}
}
@mastersthesis {83275,
	title = {Effects of Stream Restoration on Macroinvertebrate Communities in an Oregon Coast Range System},
	year = {1996},
	note = {"This research evaluates two types of fish habitat restoration: off-channel structures (alcoves) and in-channel structures (log weirs). I compared macroinvertebrate habitats and communities in natural and artificial alcoves in Upper and South Fork Lobster Creeks, Lane Co., and examined the effects of log weirs on in-channel habitat diversity, community composition, drift patterns, and fish consumption of macroinvertebrates." (from the Abstract) Color photographs.},
	pages = {100 p.},
	school = {Oregon State University},
	type = {Masters Thesis},
	edition = {M.S.},
	chapter = {Dept. of Entomology},
	address = {Corvallis, Or.},
	keywords = {Alsea River, aquatic insects, aquatic invertebrates, Bear Creek, Coho salmon =  Oncorhynchus kisutch, crustaceans, dissolved oxygen, East Fork Lobster Creek, general ecosystem description, geology, habitat restoration, habitats, J-Line Creek, Lobster Creek, logging, sediments, South Fork Lobster Creek, species list, streamflow, theses},
	url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/3f462870x},
	author = {Christensen, M. Jo}
}
@mastersthesis {24051,
	title = {Pollution and Tidal Flushing Predictions for Oregon{\textquoteright}s Estuaries},
	year = {1975},
	note = {"The overriding goal of this study was to provide first order estimates of dilution and tidal flushing of waste discharges released hypothetically into various Oregon estuaries during critical low flows and tides." (from the Abstract) Masters of Ocean Engineering thesis.  Major professor was Larry S. Slotta.},
	pages = {163 p.},
	school = {Oregon State University},
	type = {Masters Thesis},
	edition = {M. Oc. E.},
	chapter = {Dept. of Civil Engineering, Ocean Engineering},
	address = {Corvallis, Or.},
	keywords = {Alsea Bay, Columbia River estuary, Coos Bay, dissolved oxygen, Nehalem Bay, Siletz Bay, Siuslaw Bay, theses, tidal currents, tidal data, Tillamook Bay, Umpqua Bay, water pollution, Yaquina Bay},
	url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/db78tf26w},
	author = {Choi, Byungho}
}
@inbook {17436,
	title = {Effects of logging on the habitat of coho salmon and cutthroat trout in coastal streams},
	booktitle = {Symposium on Salmon and Trout in Streams},
	year = {1969},
	pages = {p.355-375},
	publisher = {Institute of Fisheries, University of British Columbia},
	organization = {Institute of Fisheries, University of British Columbia},
	address = {Vancouver, B.C.},
	keywords = {Alsea River Basin, Alsea Watershed Study, Coho salmon = Oncorhynchus kisutch, cutthroat trout = Oncorhynchus clarki, Deer Creek, dissolved oxygen, Drift Creek, Flynn Creek, human impacts, logging, natural resource management, Needle Branch, sediment data, terrestrial vegetation, water quality, water temperature},
	url = {https://www.fsl.orst.edu/rna/Documents/publications/Flynn\%20Creek_Effects\%20of\%20Logging\%20on\%20the\%20habitat_Hall.pdf},
	author = {Hall, James D. and Lantz, Richard L.},
	editor = {Northcote, T. G.}
}
@book {17531,
	title = {Alsea Watershed Study:  To Determine the Effects of Logging on Aquatic Resources},
	year = {1967},
	note = {A cooperative study by the Oregon State University and others},
	month = {1967},
	keywords = {Alsea River Basin, Alsea Watershed Study, Deer Creek, dissolved oxygen, Drift Creek, Flynn Creek, human impacts, logging, natural resource management, Needle Branch, sediment data, terrestrial vegetation, water quality, water temperature},
	url = {https://ir.library.oregonstate.edu/concern/technical_reports/jw827c46j},
	author = {Hall, James D. and Oregon State University}
}
@mastersthesis {17681,
	title = {Dissolved Silicate in Waters Offshore Oregon and in Four Adjacent Rivers},
	year = {1964},
	note = {Major Professor: Kilho Park. "Water samples from off the Oregon Coast, Yaquina and Coos Bays, the Columbia and Alsea Rivers, taken from November 1962 to February 1964, were analyzed for dissolved silicate content."},
	month = {1964},
	pages = {98 p.},
	school = { Oregon State University},
	type = {Masters Thesis},
	edition = {M.A.},
	chapter = {Dept. of Oceanography},
	address = {Corvallis, Or.},
	keywords = {Alsea River estuary, chemical, Columbia River estuary, Coos River estuary, dissolved oxygen, phosphate, salinity, silicate, theses, water temperature, Yaquina Bay},
	url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/rb68xf50q},
	author = {Matson, Adrian Luther}
}
