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The California North Coast Water Quality Control Board (CNCWQCB) and Oregon Department of Environmental Quality (ODEQ) have been working with US EPA Regions 9 and 10 on development of a hydrodynamic and water quality model of the Klamath River. The Klamath River is listed as impaired
on the Clean Water Act Section 303(d) List for nutrients, temperature, low dissolved oxygen, chlorophyll a, and pH in some or all reaches of this bi-state water, and CNCWQCB and ODEQ are developing Total Maximum Daily Loads (TMDLs) to address these impairments. The model will be used to characterize
loading capacity and aid in setting load allocations for these impairments. To characterize loading capacity, the need for a natural condition baseline scenario was identified. This scenario addresses provisions in both Oregon and California water quality standards. The State of Oregon's water
quality standards have a narrative portion which states that where a less stringent natural condition exceeds existing numeric criteria, the natural condition supersedes the numeric criteria and becomes the standard for the water body. The CNCWQCB's narrative water quality objective for temperature
calls for natural receiving water temperatures. The simplicity of a natural conditions criterion belies the complexity of its implementation. One of the few feasible tools for estimating an impaired water body's natural state is a physically based water quality model. The Klamath River TMDL
uses a water quality model to estimate the natural condition and seeks to account for anthropogenic changes to instream hydraulics and tributary / source flow and loading. This manuscript presents the approach applied in representing natural conditions of the Klamath River. Challenges in developing
this scenario have included incorporating upstream and tributary TMDLs, accounting for changes in tributary and instream flow due to irrigation, and accounting for changes in instream hydraulics due to four dams and associated power facilities. The natural conditions are estimated for flow,
temperature, dissolved oxygen, nutrients, pH and algae. In Oregon, Upper Klamath Lake is the headwaters to the Klamath River. ODEQ developed a phosphorus TMDL for the lake in 2002. Challenges in incorporating this TMDL included differing years of data and analysis and the lack of time-variable
predictions to feed key parameters for the Klamath River model. Furthermore, even under restored conditions, Upper Klamath Lake is predicted to deliver large nutrient and CBOD loads one out of every four years due to naturally occurring algal blooms, requiring a policy decision as to whether
the TMDL targets a median or extreme natural water quality condition. Natural flows were estimated using a Bureau of Reclamation natural flow study. Natural instream hydraulics for the hydropower reach were predicted using a physically based model with estimates of natural channel properties
with dams removed. In California, TMDLs have been completed for the Shasta, Scott, Salmon and Trinity Rivers, major Klamath River tributaries. As in Oregon, developing natural hydrographs in basins with dams, extensive irrigation, and out of basin water transfers constituted a major challenge;
a Bureau of Reclamation analysis of unimpaired flows combined with additional analysis of USGS gage data was used to guide estimation of natural hydrographs. Other significant challenges in boundary condition definition included extending modeling results for tributaries developed for critical
period weeks to address the full critical period, typically months in duration; and converting water quality parameter outputs from one model to match input requirements of another model. The water quality model integrates these changes and predicts a natural condition.
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