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 degrees 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 matt