Introduction


The Klamath River flows about 255 mi (410 km) from the outlet of Upper Klamath Lake to the Pacific Ocean through southern Oregon and northern California. The first 1-mile reach downstream of Upper Klamath Lake (from Link River Dam to near sampling site 11507501; fig. 1) is named Link River; the Klamath River proper begins at the mouth of Link River. Stage in the next 20 miles is controlled by Keno Dam (fig. 1). Water quality in the Link River to Keno Dam reach has been designated as “water quality limited” for exceeding ammonia toxicity and dissolved oxygen criteria year-round, and pH and chlorophyll a criteria in summer (Oregon Department of Environmental Quality, 2007). A Total Maximum Daily Load (TMDL) plan for this reach of the Klamath River (Oregon Department of Environmental Quality, 2010) was approved by the U.S. Environmental Protection Agency in May 2012. Water temperature allocations have also been established for point and nonpoint sources in this reach, due to the water temperature TMDL below Keno Dam.


Water quality in this reach is affected by hydrology, atmospheric conditions, tributaries and upstream inputs, withdrawals, instream biogeochemistry, and biota. Mechanistic computer models such as CE-QUAL-W2 (Cole and Wells, 2008) include many of these processes that affect water quality, and the models are regularly used to provide insights on the relative importance, rates, and other characteristics of the processes. Models can also be used to make predictions about the effects of system changes on water quality. The Klamath River TMDL was based in part on a CE-QUAL-W2 model for the years 2000 and 2002 (Tetra Tech, Inc., 2009; Rounds and Sullivan, 2009; Rounds and Sullivan, 2010).


The U.S. Geological Survey (USGS), Bureau of Reclamation (Reclamation), and Watercourse Engineering, Inc. (Watercourse) initiated a project in 2006 that led to an improved understanding of water-quality processes in the Link River to Keno Dam reach of the Klamath River. Two years of field data were collected in 2007 and 2008, with additional experimental work to investigate the characteristics of flow, suspended matter settling, and dissolved oxygen and organic matter dynamics (Sullivan and others, 2008, 2009, 2010; Poulson and Sullivan, 2010; Deas and Vaughn, 2011). Continuous water-quality monitoring at 12 sites by Reclamation in 2006–09 contributed valuable time-dense data for model calibration and for helping to understand water-quality dynamics in the system. A CE-QUAL-W2 model was constructed for years 2006–09 based on these extensive datasets and an improved understanding of instream processes (Sullivan and others, 2011). This USGS‑Watercourse‑Reclamation model (henceforth simply called the USGS model) was originally configured to simulate stage, flow, water velocity, ice cover, water temperature, specific conductance, inorganic suspended sediment, three algal groups, total nitrogen, total phosphorus, particulate nitrogen, particulate carbon, sediment organic matter, dissolved oxygen, dissolved organic carbon, and dissolved nitrate, ammonia, and orthophosphorus. In CE-QUAL-W2, orthophosphorus is used to model bioavailable phosphorus, which is often measured as soluble reactive phosphorus (SRP), orthophosphate, or dissolved phosphorus.


CE-QUAL-W2 is a two-dimensional model used to simulate variability from upstream to downstream and from the river surface to the channel bottom. The third dimension, from bank to bank, is considered to be well mixed in this model. The USGS upper Klamath River model grid consists of 102 segments that connect together in the direction of flow; segments average 1,009 ft (308 m) in length. Each segment represents a cross-sectional shape of the river channel, with stacked layers of varying width from the river surface to the channel bottom. Vertical layers are 2 ft (0.61 m) in height. The model runs on a variable time step that can be as short as one second, but produces output for all constituents for all layers in each segment at a user-chosen time interval, often hourly.


During the initial construction of the USGS model, the hypothesis was developed that macrophytes (rooted aquatic plants) may be an important contributor to the nutrient, pH, and oxygen cycling in the Klamath River; however, no macrophyte field data were available. Further, model development suggested that pH buffering by organic matter, orthophosphorus, and ammonia, or a combination of these, may be important in this reach, but CE-QUAL-W2 did not include equations to account for those forms of buffering. Thus, the model published in 2011 (Sullivan and others, 2011) did not simulate macrophytes and was not calibrated for pH. This study describes macrophyte field data and the addition of macrophytes to the model, the addition of enhanced pH buffering to CE-QUAL-W2, and recalibration of the upper Klamath River model for the years 2006–09.


First posted March 1, 2013