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Scientific Investigations Report 2013–5135

Prepared in cooperation with the Bureau of Reclamation

Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

By Annett B. Sullivan, I. Ertugrul Sogutlugil, Stewart A. Rounds, and Michael L. Deas

Thumbnail of and link to report PDF (3.6 MB) Significant Findings

The Link River to Keno Dam (Link-Keno) reach of the Klamath River, Oregon, generally has periods of water-quality impairment during summer, including low dissolved oxygen, elevated concentrations of ammonia and algae, and high pH. Efforts are underway to improve water quality in this reach through a Total Maximum Daily Load (TMDL) program and other management and operational actions. To assist in planning, a hydrodynamic and water-quality model was used in this study to provide insight about how various actions could affect water quality in the reach. These model scenarios used a previously developed and calibrated CE-QUAL-W2 model of the Link-Keno reach developed by the U.S. Geological Survey (USGS), Watercourse Engineering Inc., and the Bureau of Reclamation for calendar years 2006–09 (referred to as the “USGS model” in this report). Another model of the same river reach was previously developed by Tetra Tech, Inc. and the Oregon Department of Environmental Quality for years 2000 and 2002 and was used in the TMDL process; that model is referred to as the “TMDL model” in this report.

This report includes scenarios that (1) assess the effect of TMDL allocations on water quality, (2) provide insight on certain aspects of the TMDL model, (3) assess various methods to improve water quality in this reach, and (4) examine possible water-quality effects of a future warmer climate. Results presented in this report for the first 5 scenarios supersede or augment those that were previously published (scenarios 1 and 2 in Sullivan and others [2011], 3 through 5 in Sullivan and others [2012]); those previous results are still valid, but the results for those scenarios in this report are more current.

Significant findings from this study include:

  • When comparing two sets of potential water-quality improvements, one in which Upper Klamath Lake attained its TMDL target and another in which Klamath River point and nonpoint sources between Link and Keno Dams met TMDL allocations, it was found that the first had a larger beneficial effect on Link-Keno reach water quality compared to the second. For example, June to October average dissolved-oxygen concentrations increased 2.4–3.6 mg/L (54–126 percent), depending on the year, when the upstream inflow from Upper Klamath Lake was simulated at its TMDL target. In contrast, when Klamath River point and nonpoint sources met TMDL allocations, June to October average dissolved-oxygen concentrations increased by 0.1–0.24 mg/L (2–4 percent). This comparison was similar for most water-quality constituents, although both sets of improvements had notable effects on decreasing orthophosphorus concentrations in the Link- Keno reach.

  • Under base case conditions 2006–09, digressions less than the State of Oregon dissolved-oxygen criteria occurred most frequently in summer in the Link‑Keno reach. Considering the three dissolved-oxygen criteria that must be met, the 30-day criteria were most difficult to attain. The dissolved-oxygen criteria were met for the longest period in the upstream reach nearer Link River, with non-attainment periods increasing in the downstream direction toward Keno Dam, due in part to the decay of algae and organic matter through the reach.

  • Simulations with Upper Klamath Lake at its TMDL water quality target overall were more effective at reducing the number of days when dissolved-oxygen criteria were not met, compared to simulations in which Klamath River point and nonpoint sources were assumed to meet the Klamath River TMDL allocations. Setting the point and nonpoint sources at TMDL allocations was predicted to help meet the dissolved-oxygen criteria when Upper Klamath Lake also was at its TMDL target.

  • Under base case conditions, the Link-Keno reach exceeded the State of Oregon maximum pH criterion of 9.0 in summer at certain times and locations, especially in areas where algal blooms were present. Algal populations were greatest in the upstream portion of the reach, which led to more frequent pH criterion exceedances in that part of the river.

  • Although the TMDLs addressed factors such as total nitrogen, total phosphorus, and biochemical oxygen demand (BOD) for inflows and point and nonpoint sources, other water-quality constituents such as pH and total inorganic carbon (TIC) likely would change as TMDL responses are implemented, but it is more difficult to predict these future levels because they are affected by watershed conditions that lie outside the Link-Keno model domain. Simulations of Upper Klamath Lake and Link-Keno sources at TMDL targets and allocations indicated that Link-Keno model pH predictions were sensitive to boundary and point and nonpoint source estimates of pH and total inorganic carbon.

  • Under base case conditions, the acute ammonia toxicity criteria were simulated to be exceeded from 0 to 27 days per year, depending on location and year. The chronic ammonia toxicity criteria were simulated to be exceeded more frequently, between 11 and 158 days per year. Because the ammonia criteria are pH-dependent, these criteria were sensitive to the formulation of pH and TIC in the boundaries of model scenarios.

  • A qualitative comparison of the USGS and TMDL model pH simulations indicated that the USGS model more closely simulated the measured seasonal patterns in pH for years 2006-09. This is due in part to (1) the enhanced buffering capabilities added to the USGS model, which includes pH buffering by organic matter, orthophosphorus, and ammonia and (2) the inclusion of macrophytes in the USGS model.

  • Shunting, or diverting, particulate matter so that it remained in the Klamath River instead of being removed through four Klamath Project diversion canals, was predicted to worsen water quality in the Link-Keno reach as measured by the predicted concentrations of dissolved oxygen, ammonia, and chlorophyll a.

  • Model results indicated that removal of large algae and particulate organic matter at the Link River inflow could improve water quality in the Link-Keno reach, greatly increasing dissolved oxygen and decreasing nutrients and chlorophyll a. However, the downstream pH may remain high in summer. Removing material for the entire year had only a small additional benefit compared to treatment for the primary growth period of June–October. A significant fraction of the algae and particulate material would need to be removed to bring the river closer to compliance with the dissolved‑oxygen criteria.

  • Routing river water through wetlands adjacent to the Klamath River was simulated to remove particulate inorganic and organic matter, algae, and labile dissolved organic matter from the river water, leading to increases in dissolved oxygen and decreases in nutrient, organic matter, and chlorophyll a concentrations downstream of the wetland. Wetlands farther upstream in the Link-Keno reach are potentially more advantageous, as they could treat the higher levels of particulate material and algae found there.

  • Reducing Link River flows by 200 ft3/s and routing that water through the Klamath Project and back to the Klamath River through the Lost River Diversion Channel, the Klamath Straits Drain, or both was predicted to have only modest effects on water quality in the Link-Keno reach, with some improvements and some degradation depending on location and time of year.

  • Scenarios that examined the effects of reaeration and dissolved-oxygen injection revealed that these treatments are likely to be effective at increasing dissolved-oxygen concentrations in the reach, although it was predicted that such actions would have negligible short-term effects on other water-quality constituents.

  • In scenarios that focused on reducing concentrations of particulate organic matter or algae, the point of greatest improvement in dissolved oxygen was typically farther downstream of the treatment location, and may even be downstream of the lower boundary of the model at Keno Dam. In contrast, in a scenario that directly injected dissolved oxygen, the point of greatest improvement was immediately downstream of the treatment location.

  • Simulations of increased riparian shade along the Link-Keno reach produced cooling of less than 0.6°C as a reach average for June–October. Less solar radiation reaching the river also led to minor effects on other water-quality constituents that are affected by water temperature and photosynthesis.

  • Simulations of a future warmer climate with air temperature increases of 0.86–3.25°C were predicted to increase annual average water temperatures by 0.6–2.4°C in the Link-Keno reach. Warmer temperatures would lead to lower dissolved oxygen solubility and the simulations predicted dissolved-oxygen concentration decreases on the order of 0.3 mg/L as an annual average with the maximum air temperature increase of 3.25°C.

Results from these model scenarios demonstrate that large changes in river water quality can be achieved through one or more management strategies that target the most important inputs and (or) instream water-quality processes of the upper Klamath River. Future tests and refinements of the model based on research, targeted monitoring, and pilot studies of potential management actions are likely to further improve the accuracy and value of these model predictions. As potential management plans are refined, the model can be used to provide further insights about likely water-quality outcomes.

First posted July 24, 2013

For additional information contact:
Director, Oregon Water Science Center
U.S. Geological Survey
2130 SW 5th Avenue
Portland, Oregon 97201

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Suggested citation:

Sullivan, A.B., Sogutlugil, I.E., Rounds, S.A., and Deas, M.L., 2013, Modeling the water-quality effects of changes to the Klamath River upstream of Keno Dam, Oregon: U.S. Geological Survey Scientific Investigations Report 2013–5135, 60 p.,

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