Executive Summary

A hydrodynamic, water temperature, and water-quality model was constructed for a 20-mile reach of the Klamath River downstream of Upper Klamath Lake, from Link River to Keno Dam, for calendar years 2006–09. The two-dimensional, laterally averaged model CE-QUAL-W2 was used to simulate water velocity, ice cover, water temperature, specific conductance, dissolved and suspended solids, dissolved oxygen, total nitrogen, ammonia, nitrate, total phosphorus, orthophosphate, dissolved and particulate organic matter, and three algal groups. The Link–Keno model successfully simulated the most important spatial and temporal patterns in the measured data for this 4-year time period. The model calibration process provided critical insights into water-quality processes and the nature of those inputs and processes that drive water quality in this reach. The model was used not only to reproduce and better understand water-quality conditions that occurred in 2006–09, but also to test several load-reduction scenarios that have implications for future water-resources management in the river basin. 


The model construction and calibration process provided results concerning water quality and transport in the Link–Keno reach of the Klamath River, ranging from interesting circulation patterns in the Lake Ewauna area to the nature and importance of organic matter and algae. These insights and results include:


• Modeled segment-average water velocities ranged from near 0.0 to 3.0 ft/s in 2006 through 2009. Travel time through the model reach was about 4 days at 2,000 ft³/s and 12 days at 700 ft³/s flow. Flow direction was aligned with the upstream–downstream channel axis for most of the Link–Keno reach, except for Lake Ewauna. Wind effects were pronounced at Lake Ewauna during low-flow conditions, often with circulation in the form of a gyre that rotated in a clockwise direction when winds were towards the southeast and in a counterclockwise direction when winds were towards the northwest.

• Water temperatures ranged from near freezing in winter to near 30 °C at some locations and periods in summer; seasonal water temperature patterns were similar at the inflow and outflow. Although vertical temperature stratification was not present at most times and locations, weak stratification could persist for periods up to 1–2 weeks, especially in the downstream parts of the reach. Thermal stratification was important in controlling vertical variations in water quality.

• The specific conductance, and thus density, of tributaries within the reach usually was higher than that of the river itself, so that inflows tended to sink below the river surface. This was especially notable for inflows from the Klamath Straits Drain, which tended to sink to the bottom of the Klamath River at its confluence and not mix vertically for several miles downstream.

• The model was able to capture most of the seasonal changes in the algal population by modeling that population with three algal groups: blue-green algae, diatoms, and other algae. The blooms of blue-green algae, consisting mostly of Aphanizomenon flos aquae that entered from Upper Klamath Lake, were dominant, dwarfing the populations of the other two algae groups in summer. A large part of the blue-green algae population that entered this reach from upstream tended to settle out, die, and decompose, especially in the upper part of the Link–Keno reach. Diatoms reached a maximum in spring and other algae in midsummer. 

• Organic matter, occurring in both dissolved and particulate forms, was critical to the water quality of this reach of the Klamath River, and was strongly tied to nutrient and dissolved-oxygen dynamics. Dissolved and particulate organic matter were subdivided into labile (quickly decaying) and refractory (slowing decaying) groups for modeling purposes. The particulate matter in summer, consisting largely of dead blue-green algae, decayed quickly. Consequently, this particulate matter exerted a high oxygen demand over short periods and contributed strongly to low dissolved-oxygen conditions present during summer and fall. Particulate matter in winter and dissolved organic matter throughout the year was largely refractory (slow to decay). The slower decay rate of this refractory material translates to less oxygen demand over short periods, but also will manifest itself as higher oxygen demand downstream of Keno Dam.

• The decay and settling of algae and particulate organic matter in the upper part of the Link–Keno reach of the Klamath River has important implications for nutrients. Decay releases nitrogen and phosphorus from particulate forms into dissolved forms such as ammonia, which had elevated concentrations in the downstream part of this reach in summer. Dissolved nutrients showed consistent seasonal patterns that were simulated well by the model. Ammonia concentrations were highest in midsummer and winter and lowest in spring. Nitrate concentrations were highest in winter and lowest in summer. Orthophosphorus concentrations were at their maximum in midsummer and lowest in winter. Comparing modeled hourly nutrient loads at the Link River inflow and the Keno Dam outflow, the Link–Keno reach and its tributaries were a source of total nitrogen and total phosphorus to downstream reaches in early spring and a sink in summer.

• Dissolved-oxygen concentrations were near saturation in winter, but periods of supersaturation could occur in spring and early summer as oxygen was produced by algal photosynthesis. In mid- to late summer, oxygen sources were overwhelmed by oxygen sinks, especially the decay of organic matter in the water column and river bottom. Extensive anoxia occurred during this period. The sediment oxygen demand was dynamic and represented a relatively fast decomposition of materials deposited during that same year. The labile material was eventually exhausted and reaeration from the atmosphere allowed the system to slowly return towards oxygen saturation in fall. The model simulated the general temporal and spatial patterns in dissolved oxygen, although the inclusion of macrophytes and additional information on reaeration processes, organic matter, and algal dynamics could improve the simulation of dissolved oxygen.

• Calendar years 2007 and 2008 had more extensive datasets than 2006 and 2009. The models built with less extensive input data were still able to reproduce the patterns in the measured data reasonably well. These findings underline the importance of using results from the 2007 and 2008 detailed field data and experimental work to determine robust model rates, stoichiometry relations, and other parameters that can be applied successfully to years with less data and with different conditions.

• The 2006–09 models were applied to examine the effects of several reduced-loading scenarios consistent with total maximum daily load (TMDL) targets. The water quality of the Link River inflow was modified in one scenario so that it met the in-lake phosphorus targets of the Upper Klamath Lake TMDL. Point and nonpoint sources along the Klamath River were set to be in compliance with their Klamath River TMDL allocations in another scenario. Results from those scenarios indicated that dissolved-oxygen conditions improved the most when Link River loads were reduced; depending on year, average June through October dissolved-oxygen concentrations increased between 1.9 and 3.2 mg/L. Similarly, ammonia concentrations improved the most under this scenario, with an average June through October concentration decrease between 0.20 and 0.34 mg/L. Orthophosphorus concentrations were decreased significantly in both scenarios that reduced concentrations from Link River and scenarios that reduced concentrations from in-reach point and nonpoint sources, with June through October concentration decreases between 0.02 and 0.06 mg/L.


The calibrated models are useful tools that reproduce the most important water-quality processes occurring in the Link–Keno reach of the Klamath River. These models are accurate enough to provide insights into the nature of those processes and the probable effects of proposed management and water-quality improvement strategies.


First posted July 14, 2011