Klamath Basin: A Watershed Approach to Support Habitat 

Restoration, Species Recovery, and Water Resource Planning 

Water allocation among human and natural resource uses in 

the American West is challenging. Western rivers have been 

largely managed for hydropower, irrigation, drinking water, 

and navigation. Today land and water use practices have 

gained importance, particularly as aging dams are faced with 

re-licensing requirements and provisions of the Endangered 

Species and Clean Water Acts. Rising demand for scarce water

heightens the need for scientific research to predict

consequences of management actions on habitats, human 

resource use, and fish and wildlife. Climate change, 

introduction of invasive species, or restoration of fish passage 

can have large, landscape-scaled consequences— research must

expand to encompass the appropriate scale and by applying 

multiple scientific disciplines to complex ecosystem challenges 

improve the adaptive management framework for decisionmaking. 

The Klamath River Basin embodies intense challenges and has 

gained national attention in federal and state resource management 

planning. Decreasing water availability during drought, fish dieoffs, degraded water quality, and closures of commercial salmon 

fisheries, all underscore the need for relevant research, improved 

predictive river models, and tools to evaluate the effects of 

alternative management actions on groundwater and river systems 

and their associated biota. Relicensing of dams on the Klamath 

River could lead to reintroduction of Pacific salmon to significant 

parts of their former range within the basin. An expanded USGS 

science agenda is responding to growing public support for 

watershed-scale science that addresses Klamath Basin concerns. 

The Klamath River originates in southcentral Oregon, downstream of Upper 

Klamath Lake, and flows 263 miles to 

the Pacific Ocean. Upper Klamath 

Lake is the primary irrigation supply

for the Bureau of Reclamation’s 

Klamath Project. The Klamath Basin 

covers slightly more than 10 million 

acres, including about 6.1million acres 

of public land, 90,000 acres of tribal 

land and 3.8 million acres of private land. Iron Gate Dam is 

the commonly recognized dividing point between the upper 

and lower basins. Four additional dams that provide 

hydropower and irrigation water to the upper basin are 

located between Upper Klamath Lake and Iron Gate Dam. 

The upper basin is relatively dry and covers 8,060 square 

miles, while the lower basin is wetter and covers 7,628 square 

miles. 

Headwaters to Ocean 

Geographic, Geologic, and Hydrologic Setting 

U.S. Department of the Interior USGS FS -2007-3068 

U.S. Geological Survey August 9, 2007 
A Strong Foundation of USGS Science in the 

Klamath Basin 

The USGS has been a major science provider to the 

Department of the Interior and other resource managers in 

the Klamath Basin since the early 1990s. Interior and tribal 

managers use USGS data and findings to make 

economically sustainable and environmentally sound 

natural resource decisions. 

Work in the Upper Klamath Basin has focused on science 

to support management of water quantity, quality, and 

endangered Lost River and shortnose suckers. Recent 

USGS studies have: 

• Examined aquifer hydrogeology, ground-water 

recharge, and the impacts of increasing ground 

water use; 

• Improved forecasts of flows into Upper Klamath 

Lake to improve management of irrigation, lake 

levels, and downstream flows; 

• Shown how water quality is influenced by lake 

levels, wetland management, and climate 

conditions; and 

• Assessed the quality of stream-channel habitat to 

guide restoration activities. 

The Lower Klamath Basin encompasses diverse waterrelated issues affecting the health and survival of salmon 

and other fish species. In recent years, large numbers of

coho and Chinook salmon have been infected by a parasite 

while migrating to sea as juveniles. In 2006, the lack of 

returning adult salmon to the Klamath River resulted in the 

closure of several hundred miles of Pacific Coast salmon 

fisheries. These conditions served to highlight the need for 

an ecosystem-based understanding of stressors affecting fish 

in the river. The status of other fishes such as steelhead, 

green sturgeon, lampreys, and coastal cutthroat trout are 

also of high concern. The physical and biological effects of 

variable flow regimes in the lower river on fish distribution, 

abundance, and migratory behavior are critical issues being 

investigated by USGS. 

Future Science Directions 

The USGS has established research objectives to answer the 

critical science needs of federal, state and Tribal 

stakeholders in the Klamath Basin. These objectives 

address the impact of human activities on the changing 

Klamath ecosystem. Moreover, the objectives spring from

research forefronts envisioned in the recent USGS 

publication: “Facing Tomorrow’s Challenges: USGS 

Science in the Coming Decade.” They embrace the 

Department of the Interior’s recently released policy and 

publication: “Adaptive Management Technical Guide” 

which champions a strong and continuing linkage between 

science and natural resource decision-making. 

Lost River suckers spawning in nearshore areas of Upper Klamath 

Lake.

Recently, the USGS has engaged a diverse community of 

Klamath Basin stakeholders to help identify information 

needs and science priorities. While science priorities still 

address species recovery, habitat restoration, and water 

availability, past scientific investigations proceeded issueby-issue, and treated the Upper and Lower Klamath Basins 

as separate entities. Today, connections between these subbasins through biological and physical linkages—with water 

as the key ecological integrator—are the driving force in 

ecosystem scale planning. Basin-wide scaling of 

investigative approaches will be a critical component of 

future USGS research and monitoring in the Klamath Basin. 

Four biological issues have emerged as high priorities 

within the Klamath ecosystem:

• Fish health and disease ecology

• Wetland restoration 

• Riverscape ecology and predictive modeling 

• Reintroduction of Pacific salmon 

Supporting these biological needs are three-broad physical 

science priorities: 

• Coupled ground-water/surface-water modeling 

• Nutrient dynamics and algal processes 

• Water flow and channel modeling 

By addressing these priorities, the USGS will make 

significant contributions toward: 

• Developing and evaluating restoration strategies for 

adaptive management; 

• Predicting changes in riverine habitats and aquatic 

organisms in response to variable environmental 

conditions; 

• Predicting ecosystem responses to climatic change; 

and 

• Forecasting water availability and predicting 

consequences of management actions. 
upstream spawning habitat for the endangered suckers.

Models predicting the outcome of management alternatives 

will enable managers to find the most effective course for 

restoration before implementing field projects. Ongoing 

scientific feedback to facilitate adaptive management 

among scientists and managers will allow improvement and 

refinement of restoration actions as they progress. 

Riverscape Ecology and Predictive Modeling 

The USGS River Ecosystem and Modeling Science 

(REMS) initiative is being designed to provide managers 

and the public with: 

• Insight into the natural water quality and quantity 

variability and water transport processes; 

• Up-to-date information on the impacts of human 

water use; and 

• The capability to predict how water use, supply, and 

quality influence aquatic ecosystems. 

State-of-the-art technologies will be employed to develop 

predictive models that will include decision support systems 

to assess the environmental consequences of alternative 

management strategies and will be adaptable to other large 

river systems.

Reintroduction of Salmon 

Federal Energy Regulatory Commission (FERC) relicensing of some Klamath River dams will require passage 

for migratory salmon that were excluded for many decades 

from the Upper Basin by the original dams. Re-introduction 

of anadromous salmon above Iron Gate Dam represents a 

major restoration priority to tribes, recreational and 

commercial fishers, and natural resource managers. Key 

information needs include fish passage, habitat suitability in 

upper basin streams, migration and seasonal rearing in 

Upper Klamath Lake, interactions with resident fish species, 

disease ecology, stock selection, and habitat conditions in 

the lower Klamath River. 

Restoration of the Williamson River Delta on Upper Klamath Lake. 

USGS will address pressing science priorities, partly

through a process of ecological modeling that incorporates 

functional linkages, ecological scaling, and large-scale

external drivers such as climate change. While research on 

specific issues needed by resource managers will continue, 

future investigations will be designed to answer short-term

questions that support long-term, large-scale adaptive 

management of the basin ecosystem. 

Fish Health and Disease Ecology 

Disease outbreaks have resulted in fish die-offs in both the 

Upper and Lower Klamath River Basins. In the Upper 

Basin, losses of adult shortnose and Lost River suckers have 

been caused by indigenous fish pathogens when the fish 

became stressed by poor water quality. The effects of fish 

condition and environmental stressors on disease resistance 

and survival of juvenile suckers in their first year of life are 

largely unknown, but could be critical to sustain the overall 

population. Similarly, highly visible disease-related 

mortalities of adult Chinook salmon in the Lower Klamath 

River occurred when fish were stressed by low flows and 

warm water temperatures. Infections seen in juvenile 

Chinook and other salmon are believed to be due to altered 

habitats. The Klamath Basin has gained national attention as 

a good example of how water availability, habitat 

conditions, and species relationships can influence the 

management of water for fisheries, agriculture and other 

human uses significant to regional and local economies. 

Evaluation of Wetland Restoration

Wetland and riparian restoration in the Klamath Basin is 

ongoing and more is planned. Research and monitoring is 

needed to determine if these restoration projects improve 

water quality and habitat as designed. Ultimately, managers 

need to know if their actions increase fish production or 

otherwise benefit the ecosystem. For example, removal of 

Chiloquin Dam on the Sprague River, a major headwater 

tributary of Upper Klamath Lake, will require 

multidisciplinary scientific support to successfully restore 

USGS biologist displays a 

shortnose sucker captured

at the Chiloquin Dam fish 

ladder (top right). 

A Lost River sucker captured 

at the Williamson River weir

(bottom left). 
USGS Science to Support Natural Resource Management, 

Regulatory and Policy Decisions in the Klamath Basin

Habitat 

• Klamath river flow/temperature/habitat 

modeling 

• Lake level effects on sucker habitat 

• Wood River wetlands restoration monitoring 

Water Availability

• Ground water availability/dynamics 

• Impacts of ground-water pumping on 

streamflows 

• Withdrawals and allocation – pilot water bank 

performance 

• Impoundments 

Water Management 

• Refining flow data for project management 

• Flow forecasting 

• Lake level 

• Refuge water use 

Water Quality

• Lake nutrient/algae dynamics 

• Downstream impacts on Klamath River

• Water quality of inflows and river mainstem, 

e.g. TMDL 

Dams 

• FERC re-licensing, mainstem

• Chiloquin Dam investigation (planned 

removal 2008) 

Fish Populations 

• Habitat requirements and use 

• Fish population responses to changes in 

aquatic habitat 

• Sucker population indices/dynamics as 

indicators of habitat quality

Fish Health 

• Basin integrated fish health as indicator of 

habitat quality

• Sucker physiological and behavioral 

responses to water quality 

Nutrient Dynamics and Algal Processes 

Each summer large blooms of the blue-green alga 

Aphanizomenon flos-aquae (AFA) in the Upper Klamath 

Lake, lead to low dissolved oxygen and lethal conditions 

for endangered suckers. Major die-offs of suckers 

occurred in 1986, 1995, 1996, and 1997. In order to

assess the remediation strategies, which range from

dredging to chemical treatments, the lake bottom will be 

mapped in detail to determine the nutrient forms and the 

degree and depth of sediment enrichment. Preliminary

data indicate the presence of “hot spots” that could be 

targeted for remediation. 

Water Flow and In-Channel Modeling 

Natural cycles of flooding and sediment transport have

been significantly altered in the Klamath Basin by dams 

and water diversion. Channel shape, bedform substrate, 

nutrient cycling, vegetation type, and aquatic communities 

have changed as a result of flow regulation. These factors 

in turn affect aquatic habitat suitability for key biota. The 

USGS will use a sophisticated hydrodynamic model of

multiple geomorphologic processes in the Klamath and 

For additional information, please contact:

Frank Shipley, Ph.D. 

U.S. Geological Survey

Office of the Regional Executive for Biology

909 First Ave 8th Floor 

Seattle, WA 98104 

Phone: (206) 220-4600 

FAX: (206 220-4624 

Coupled Ground-Water/Surface-Water 

Watershed Model

As a key USGS scientific priority, climate change will be 

important in western semi-arid landscapes like the 

Klamath Basin. A variety of data and predictive tools 

already exist to improve hydrologic forecasts in the 

Klamath Basin. The challenge will be linking these 

diverse models and data streams into a single tool. The 

USGS release of a new flow model, GS-Flow, provides 

the necessary framework to link these capabilities so 

managers and researchers can forecast hydrologic 

responses in the basin on temporal scales of weeks to 

decades. Model outputs will be linked with habitat 

suitability curves for endangered species and bioenergetics 

models of fish growth to predict multiple fish population 

responses to various hydrologic changes. 

Sprague rivers to predict fishery and other ecosystem

responses to various management scenarios such as 

restoration of vegetation, augmentation of base flows, 

restoration of peak flows, reduction of nutrient loads, and 

climate change. 

Algal bloom conditions in Upper Klamath Lake.