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Scientific Investigations Report 2012–5062

Groundwater Simulation and Management Models for the Upper Klamath Basin, Oregon and California


The upper Klamath Basin spans the Oregon-California border from the flank of the Cascade Range eastward to the high desert (fig. 1). Although much of the basin is high desert, the area receives considerable runoff from the Cascade Range, which forms the western margin, and from the volcanic uplands along the eastern margin. As a result, the area has numerous perennial streams, large shallow lakes, and extensive wetlands. Water in the basin supports irrigation, extensive waterfowl refuges, and aquatic wildlife in lakes and streams throughout the basin.

The agricultural economy of the upper Klamath Basin relies on irrigation water. Just over 500,000 acres are irrigated in the upper Klamath Basin, about 190,000 acres of which are within the Klamath Project developed and operated by the Bureau of Reclamation (Reclamation) (Burt and Freeman, 2003; Natural Resources Conservation Service, 2004). The principal source of water for the Bureau of Reclamation Klamath Project is Upper Klamath Lake. In recent years, Endangered Species Act biological opinions have required Reclamation to maintain certain lake levels in Upper Klamath Lake to protect habitat for endangered fish (specifically the Lost River sucker [Deltistes luxatus] and shortnose sucker [Chasmistes brevirostris]) and at the same time maintain specified flows in the Klamath River downstream of the lake to provide habitat and suitable conditions for salmon federally listed as threatened. This shift in water management has resulted in increased demands for water. Owing to the limitations of other options, the increased demand has resulted in increased use of groundwater in the basin. The problems associated with increased demands are, of course, exacerbated by drought.

The upper Klamath Basin has a substantial regional groundwater system, and groundwater has been used for irrigation for many decades in certain areas. The changes in water management described above coupled with a series of drier than average years resulted in an approximately 50-percent increase in groundwater pumping between 2000 and 2004 (Gannett and others, 2007). Most of this increase is focused in the area of the Klamath Project. Increased pumping has caused local water-level declines that have been problematic for some groundwater users and have generated concern among resource management agencies and the community. In addition to the measured effects, basic physics requires that the volume of groundwater pumped and used consumptively must ultimately be offset by changes in flow to or from other boundaries including streams (Theis, 1940).

The effects of large-scale groundwater pumping can spread beyond the pumping centers to other parts of the regional groundwater system. Prior to this study, the groundwater hydrology had been studied only in separate parts of the basin, with many areas left undescribed. Therefore, there was no basic framework with which to understand the potential regional effects of groundwater development in the basin and the broad ramifications of water-management decisions. In 1999, the U.S. Geological Survey (USGS) and the Oregon Water Resources Department (OWRD), with assistance from Reclamation, began a cooperative study to quantitatively characterize the regional groundwater system in the upper Klamath Basin and develop a computer model to simulate regional groundwater flow that can be used to help understand the resource and to test management scenarios. This report summarizes the development of the regional groundwater flow model and provides example applications.

Study Objectives

The principal objective of the work described in this report was to provide a numerical model that can be used for the quantitative evaluation of the regional groundwater system in the upper Klamath Basin. The ability to provide quantitative insight into the effects of groundwater pumping on hydraulic heads and discharge to streams, and the response of the groundwater system to decadal climate fluctuations and long-term climate changes was of particular interest. An additional objective was to couple the regional groundwater flow model with a groundwater management model using optimization techniques to identify ways in which groundwater management objectives can be achieved while maintaining hydraulic heads and groundwater discharge rates at needed levels. 

Purpose and Scope

The purpose of this report is to describe the development of the upper Klamath Basin regional groundwater flow model and groundwater management models, and to provide example applications. It is intended to help resource managers and other interested parties understand the basic attributes of the models, how they relate to the groundwater hydrology, how they incorporate aspects of groundwater use and water management, and to provide a basic understanding of the theory and application of coupled simulation and groundwater management models.

This report briefly describes basic modeling concepts and governing equations, but for a more thorough discussion the reader should refer to a basic groundwater modeling text such as Anderson and Woessner (1992). Much of the report is devoted to the ways in which the basic aspects of the regional groundwater system described by Gannett and others (2007) are represented in the model. The report includes a description of the numerical flow model, its spatial and temporal discretization, the representation of the geologic framework, data and methods used for model calibration, and evaluation of calibration results. The report also includes a discussion of the basic theory of groundwater management models and techniques of constrained optimization in the context of groundwater management in the upper Klamath Basin. Example simulations are included to demonstrate the capabilities of coupled flow and management models.

Study Area Description

The upper Klamath Basin (fig. 1) comprises the entire drainage basin above Iron Gate Dam, including the internally drained Lost River subbasin and Butte Valley area, and encompasses about 8,000 mi2. Study-area and model boundaries were defined to correspond to hydrologic boundaries across which groundwater flow can be estimated or assumed to be negligible. The southwestern boundary near Iron Gate Dam was selected because it corresponds with the transition from a geologic terrane dominated by permeable volcanic rock to a terrane dominated by older rock with much lower permeability. There is no significant regional groundwater flow across this geologic boundary. 

The boundary between the regional flow systems in the upper Klamath Basin and the Deschutes and Fort Rock Basins to the north (not shown in fig. 1) is defined by a surface-water divide that roughly corresponds to the groundwater divide. This boundary is likely permeable. The boundary between the groundwater system of the upper Klamath Basin and that of the Pit River basin to the south (not shown in fig. 1) also is defined by a surface-water divide in most places. The southern surface-water divide does not correspond to a groundwater divide in all places, as hydraulic head data indicate that there is southward flow of groundwater from the upper Klamath Basin south of the Tule Lake subbasin toward the Pit River basin (Gannett and others, 2007). The eastern study-area boundary corresponds to a surface-water divide and is characterized in many places by a transition to older low‑permeability geologic strata.

The upper Klamath Basin occupies a broad, faulted, volcanic plateau that spans the boundary between the Cascade Range and the Basin and Range geologic provinces. The basin is bounded by the volcanic arc of the Cascade Range on the west, the Deschutes River basin to the north, internally drained basins to the east, and the Pit River basin to the south. The elevation of the Cascade Range along the western margin ranges from 5,000 to 7,000 ft with major peaks, such as Mount McLoughlin and Mount Thielsen, exceeding 9,000 ft. The interior parts of the basin are dominated by northwest‑trending fault-bounded basins, typically several miles wide, with intervening uplands. Basin floors range in elevation from roughly 4,000 to 4,500 ft, and adjoining fault‑block upland elevations range from 4,500 to more than 5,000 ft. The northern and eastern parts of the upper Klamath Basin consist of a volcanic upland with numerous eruptive centers, including Yamsay and Gearhart Mountains, both of which exceed elevations of 8,000 ft. The southeastern margin of the upper Klamath Basin consists of a broad, rugged, volcanic upland known as the Modoc Plateau, where most of the land‑surface elevations range from 4,500 to 5,000 ft. The southern margin of the basin is marked by the broad shield of Medicine Lake Volcano, which reaches an elevation of 7,913 ft.

The upper Klamath Basin is semiarid because the Cascade Range intercepts much of the moisture from the predominantly eastward moving Pacific weather systems. Mean annual precipitation (1961–90) ranges from 65.4 in. at Crater Lake National Park in the Cascade Range to 11.1 in. at Tulelake, California (Western Regional Climate Center, 2006) (fig. 2). Most precipitation occurs in the fall and winter. November through March precipitation accounts for 71 percent of the total at Crater Lake and 64 percent of the total at Klamath Falls. Most precipitation falls as snow at high elevations. The interior parts of the basin are very dry during the spring and summer; mean monthly precipitation at Klamath Falls is less than 1 in. from April through October. Winters generally are cold, with January mean-minimum and mean-maximum temperatures of 20.3 and 38.8 °F, respectively, at Klamath Falls and 17.5 °F and 34.5 °F, respectively, at Crater Lake. Summers, in contrast, are warm, with July mean minimum and maximum temperatures of 50.8 °F and 84.6 °F, respectively, at Klamath Falls and 39.8 °F and 68.0 °F, respectively, at Crater Lake.

Principal streams in the upper Klamath Basin include the Williamson River, which drains the northern and eastern parts of the basin; the Sprague River (a tributary to the Williamson), which drains part of the eastern side of the basin; the Lost River, which drains the southeastern part of the basin; and the Klamath River (fig. 1). The Lost River subbasin is actually a closed stream basin. Prior to development, the Lost River flowed to internally drained Tule Lake, although it occasionally received flow from the Klamath River during floods. The Lost River is now diverted just downstream of Olene into a channel across a low divide to the Klamath River. Generally, little water from the Lost River drainage upstream of the diversion channel now flows to the Tule Lake subbasin. Tule Lake is now largely drained except for two connected areas known as the Tule Lake sumps (fig. 1). The largest lake in the basin is Upper Klamath Lake, which has a surface area between 100 and 140 mi2 (including non-drained fringe wetlands) depending on stage (Hubbard, 1970; Snyder and Morace, 1997). Principal tributaries to Upper Klamath Lake include the Williamson River, the Wood River (which originates at a series of large springs north of the lake), and several streams emanating from the Cascade Range.

The 250-mi-long Klamath River begins at the outlet of Upper Klamath Lake, which is controlled by a dam. For the first mile downstream of the lake, the river is known as the Link River. About 1 mi downstream of the dam, the river flows into a 20-mi-long narrow reservoir behind the dam at Keno known as Lake Ewauna. John C. Boyle Reservoir and its dam are about 10 mi downstream of Keno. Below John C. Boyle Reservoir, the river enters a narrow canyon and flows freely about 20 mi to Copco Lake (a reservoir) and immediately below that, Iron Gate Reservoir. Iron Gate Dam, which impounds Iron Gate Reservoir at about river mile 190, marks the downstream boundary of the upper Klamath Basin. There are no impoundments on the Klamath River downstream of Iron Gate Dam.

The surface hydrology of the upper Klamath Basin has been extensively modified by drainage of lakes and wetlands for agriculture and routing of irrigation water. Prior to development, the Tule Lake and Lower Klamath Lake subbasins contained large lakes fringed by extensive wetlands. Prior to development of the Bureau of Reclamation Klamath Project, the high stage of Tule Lake was about 4,060 ft (La Rue, 1922). At this stage, the lake would cover an area exceeding 150 mi2. Historical accounts indicate that at high stage Tule Lake drained into the lava flows along the southern margin. In the early 1900s, the U.S. Reclamation Service (predecessor to the Bureau of Reclamation) experimented with augmenting this subsurface drainage in early attempts to drain the lake. La Rue (1922) reasoned that because the water of Tule Lake was fresh and not saline, the lake “in the past had an outlet.” Subsurface drainage also is suggested by the hydraulic head gradient that slopes southward away from the Tule Lake subbasin toward the Pit River Basin. In 1912, a canal and dam were completed that allowed the diversion of water from the Lost River to the Klamath River, cutting off the supply of water to Tule Lake. Most of Tule Lake was drained and is now under cultivation. The only remnants of the lake are the Tule Lake sumps in the southern and western parts of the basin that collect irrigation return flow. Since 1942, water from the sumps has been pumped via a tunnel through Sheepy Ridge into the Lower Klamath Lake subbasin. The Lower Klamath Lake subbasin once held a large lake-marsh complex that covered approximately 88,000 acres, about 58,000 acres of which were marginal wetlands with the remaining 30,000 acres open water (La Rue, 1922). Lower Klamath Lake was connected to the Klamath River through a channel known as the Klamath Strait, and probably through the expansive wetland that separated the lake from the river elsewhere. In the early 1900s, an earth-fill railroad bed was constructed across the northwestern margin of the Lower Klamath Lake subbasin, cutting off flow between the lake and river except at the Klamath Strait. In 1917, the control structure built into this impoundment at the Klamath Strait was closed, cutting off flow to the lake. As a result, Lower Klamath Lake is now largely drained, with much of the former lakebed and fringe wetlands under cultivation. Areas of open water remain in the Lower Klamath Lake Wildlife Refuge in the southern part of the subbasin.

Currently (2011), about 500,000 acres of agricultural land are irrigated in the upper Klamath Basin, roughly 190,000 of which are included in the Bureau of Reclamation Klamath Project (Carlson and Todd, 2003; Natural Resources Conservation Service, 2004). This total does not include wildlife refuge areas within the Project.

The upper Klamath Basin is mostly forested (Loy and others, 2001). Forest trees in upland areas east of the Cascade Range are predominantly ponderosa pine, with areas of true fir and Douglas fir on Yamsay and Gearhart Mountains. Forests in the Cascade Range primarily comprise mountain hemlock and red fir. Lower elevation uplands are dominated by lodgepole pine. Lowland forests consist largely of juniper and sagebrush with some juniper grasslands. Stream valleys and the broad, sediment-filled structural basins generally have extensive marshes, such as Sycan Marsh and Klamath Marsh, except at lower elevations, where the basins have been mostly converted to agricultural land (for example, the Wood River Valley, and the Lower Klamath Lake and Tule Lake subbasins).

Irrigation water comes from various sources in the upper Klamath Basin. Upstream of Upper Klamath Lake, in the Williamson, Sprague, and Wood River drainages, private (non-Project) irrigation water primarily comes from diversion of surface water from the main stem streams or tributaries. A smaller amount of irrigation water is pumped from wells, particularly in the Sprague River Valley and Klamath Marsh areas. In the Langell and Yonna Valleys of the upper Lost River subbasin, irrigation water comes from Clear Lake and Gerber Reservoirs. Irrigators use groundwater and some surface water in Swan Lake Valley. Groundwater is used for irrigation in areas not served by irrigation districts and to supplement surface-water supplies throughout the area. 

South of Upper Klamath Lake, most irrigation water comes from the lake, which is the largest single source of irrigation water in the upper Klamath Basin. This area is the main part of the Bureau of Reclamation Klamath Project. Water is stored in and diverted from the lake to irrigate land south of Klamath Falls, including the Klamath Valley, Poe Valley (in the Lost River subbasin), and the Lower Klamath and Tule Lake subbasins. Irrigation return flow (water that originates in Upper Klamath Lake) that ends up in the Tule Lake sumps is pumped through Sheepy Ridge and used for irrigation and refuge purposes in the southern part of the Lower Klamath Lake subbasin. Water diverted from the Klamath River several miles downstream of the lake also is used for irrigation and refuges in the Lower Klamath Lake subbasin. Irrigation and refuge return flow in the Lower Klamath Lake subbasin is routed through a series of pumping stations back to the Klamath River.

A certain amount of groundwater is used for irrigation on land surrounding the Klamath Project upslope of the major canals. Principal areas of groundwater use surrounding the Project area include the southern end of the Klamath Hills, parts of the Klamath Valley, and the northern and eastern margins of the Tule Lake subbasin (fig. 1). Some groundwater traditionally has been used for supplemental irrigation in the Project area. Increased water demand due to drought and requirements for a 100,000 acre-ft pilot water bank to be administered by Reclamation as required by the National Oceanic and Atmospheric Administration Fisheries 2002 biological opinion (National Marine Fisheries Service, 2002) have resulted in a marked increase in groundwater pumping in and around the Klamath Project since 2001 (Gannett and others, 2007).

First posted May 5, 2012

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

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