Introduction


Background


The Klamath River flows about 255 mi (410 km) from the outlet of Upper Klamath Lake through southern Oregon and northern California to the Pacific Ocean. The first 1-mi reach, just downstream of Upper Klamath Lake, is named Link River (fig. 1). The Klamath River proper begins at the mouth of Link River, and river stage in the next 20 mi is controlled by Keno Dam. Water quality in the Link River to Keno Dam reach of the Klamath River has been classified as “very poor” by the State of Oregon (Mrazik, 2007) and was designated as “water quality limited” on the State of Oregon’s 303(d) list for exceeding ammonia and dissolved-oxygen criteria throughout the year, and pH and chlorophyll a criteria in summer (Oregon Department of Environmental Quality, 2007). Although no numeric temperature criteria has been set for this reach, allocations have been established for the various inflows to the reach to address the in-reach cool water criterion and the cold water total maximum daily load (TMDL) criterion downstream of Keno Dam. Fish die-offs in summer are not uncommon (W. Tinniswood, Oregon Department of Fish and Wildlife, written commun., 2006), and are noted to occur during conditions with poor water quality.


Concerns for aquatic life are driving efforts to improve water quality in this reach. A TMDL process is underway that will specify nutrient and temperature allocations to point and nonpoint sources along this reach. The U.S. Geological Survey Oregon Water Science Center (USGS), the Bureau of Reclamation Klamath Basin Area Office (Reclamation), and Watercourse Engineering, Inc. began a study in 2006 to better understand the water quality and the processes controlling water quality in the Klamath River upstream of Keno Dam, with an ultimate goal of constructing accurate and predictive hydrodynamic, water temperature, and water quality models for the 2006–09 period. The field dataset collected for this study (Sullivan and others, 2008, 2009) was critical for model construction and calibration, and the experimental studies (Poulson and Sullivan, 2010; Sullivan and others, 2010; Deas and Vaughn, 2011) contributed to a better understanding of some of the dominant water quality processes in this reach. The resulting models allow the effectiveness of various options for improving water quality to be evaluated in a quantitative and reliable manner.


Several previous efforts to model this complex river reach have been completed. The first CE-QUAL-W2 models of this reach were developed by CH2M-Hill and Portland State University (CH2M-Hill and Wells, 1995) for years 1990 and 1992. Watercourse Engineering, Inc. (2003; PacifiCorp, 2005) used portions of those models as a basis for constructing a CE-QUAL-W2 model of this reach for calendar years 2000–2004, as part of an effort to model 250 mi of the Klamath River from Link Dam to near its discharge to the Pacific Ocean. That model was constructed to support an application to the Federal Energy Regulatory Commission by PacifiCorp for hydropower relicensing. Tetra Tech (2009) used the Watercourse model as a basis for developing a version of the Klamath River model for calendar years 2000 and 2002 to support TMDL development. However, the datasets used to develop these earlier Link River to Keno Dam models were not sufficient to capture some of the fundamental characteristics of processes and constituents (such as organic matter) driving water quality in this reach (for example, Rounds and Sullivan, 2009, 2010). To better understand and predict some of the major drivers of water quality in this reach, new datasets and models were needed.


Purpose and Scope


The purpose of this study was to develop a model of the Klamath River from Link River to Keno Dam that could (1) simulate stage, flow, velocity, temperature, and water quality, (2) provide information on processes that control water quality, (3) provide insight that would aid in the development of water quality monitoring plans, and (4) predict changes in velocity, temperature, and water quality that are likely to occur under various management and water quality improvement scenarios. This report addresses the first three goals and begins on the fourth; plans for the simulation of a range of additional scenarios is underway.


Separate models were developed for calendar years 2006, 2007, 2008, and 2009. All models were built using version 3.6 of the CE-QUAL-W2 flow and water-quality model. The models were calibrated for stage, flow, water velocity, ice cover, water temperature, inorganic suspended sediment, three algal groups (blue-green, diatom, other), total nitrogen, particulate nitrogen, nitrate, ammonia, total phosphorus, orthophosphorus, particulate carbon, and dissolved organic carbon.


Environmental Setting


The upper Klamath River lies on a broad volcanic plateau between the Cascade Range to the west and the Basin and Range province to the east (Gannett and others, 2007). The climate is semiarid, with dry summers; most precipitation occurs in fall and winter. Upper Klamath Lake is just upstream of the study reach (fig. 1); it is a large 89.6 mi² (232 km²), shallow [full pool mean depth 9 ft (2.8 m)] lake that tends to have dense summer blooms of the blue-green alga Aphanizomenon flos-aquae (AFA). Studies of sediment cores taken from the lake indicate that the lake historically was eutrophic, with a more recent shift to hypereutrophic conditions (Eilers and others, 2003; Bradbury and others, 2004). Link River Dam was constructed at the lake outlet in 1921, and in combination with partial removal of a bedrock sill, allowed a larger range of lake storage to be controlled for hydropower and irrigation diversion, as well as management of downstream flows in the Klamath River. In recent years, Link River Dam has been used to maintain the stage in Upper Klamath Lake at levels specified by Biological Opinions to protect two species of endangered fish: the Lost River sucker (Deltistes luxatus) and the shortnose sucker (Chasmistes brevirostris).


Link River flows for approximately 1 mi downstream of Link River Dam to the start of the Klamath River at Lake Ewauna, a wide and shallow area near Klamath Falls, Oregon (fig. 1). Channel widths in Lake Ewauna can approach 2,500 ft (about 800 m); in the rest of the reach down to Keno Dam, channel widths are 300–1,000 ft (about 100–300 m). Channel depths in the Link River to Keno Dam reach range up to approximately 20 ft (6 m). Studies of core samples have determined that organic matter, including wood chips from historical wood processing operations, is common on the river bottom, especially at the upper end of the reach. Locally, bedrock is close to the river bottom, especially near Keno (Eilers and Raymond, 2003; Raymond and Eilers, 2004; Eilers and Raymond, 2005).


The major inflow to the reach is at Link River (table 1). Other inflows in 2006–09 include Klamath Straits Drain and three point sources with National Pollutant Discharge Elimination System (NPDES) permits. These include two wastewater treatment plants (WWTP; Klamath Falls and South Suburban) and Columbia Forest Products (fig. 1). Gaged outflows include withdrawals through the Ady and North Canals to supply water for irrigation and wildlife refuges, and flow through Keno Dam to downstream reaches of the Klamath River. The Lost River Diversion Channel conveys water between the Klamath and Lost River systems. Water can be conveyed through the Lost River Diversion Channel in either direction, but typical operations include diversion to the Klamath River in the winter and diversion from the Klamath River in the summer.


The blue-green algae AFA was the most common algae in this part of the upper Klamath River from early summer into fall; the source of most AFA was from Upper Klamath Lake (Sullivan and others, 2008, 2009). Diatoms were at their maximum during spring and other algae, including cryptophytes and green algae, were present during various times of the year. The most frequently identified zooplankton in 2007–08 were cladocerans, copepods, and rotifers, especially Daphnia pulicaria, Chydorus sphaericus, copepod nauplii, cyclopoid copepodites, Keratella hiemalis, and Euchlanis dilatata. Fish species in the reach during a 2002–03 survey include fathead minnow (Pimephales promelas), blue chub (Gila coerulea), tui chub (Gila bicolor), shortnose sucker, and Lost River sucker among others (Terwilliger and others, 2004). Although anadromous fish are no longer present, this reach has historically supported such fish runs, and the reintroduction of Chinook salmon (Onchorhynchus tshawytscha) is being studied (Dunsmoor and Huntington, 2006; Oregon Department of Fish and Wildlife, 2008).


Keno Dam, approximately 20 mi downstream of Link River, is a stage- and flow-regulating facility constructed in 1967 (replacing a previous regulation facility) at the location of a natural basalt structure. Normal full pool elevation at Keno Dam is 4,085 ft (1,245 m) above sea level, and the total storage capacity of this reach is reported as 18,500 acre-ft (22.8 million m³) (PacifiCorp, 2002). Four other dams downstream on the Klamath River are being considered for removal, but Link River Dam and Keno Dam are slated to remain to regulate stage and flow.


First posted July 14, 2011