Following a wet winter, bulrush is shown growing in Malheur Lake. Emergent vegetation like bulrush provides nesting habitat and food resources for birds.
Oregon Water Science Center's Malheur Lake Portfolio
Active
By Oregon Water Science Center
February 20, 2026
USGS scientists have partnered with local groups to learn about the processes affecting turbidity in Malheur Lake. Located in southeastern Oregon, Malheur Lake and the surrounding refuge provide critical habitat to birds migrating along the Pacific Flyway.
Media
Sources/Usage: Public Domain. View Media Details
Overview:
Malheur Lake is the largest lake in the Harney Basin in southeastern Oregon and is located within the Malheur National Wildlife Refuge (MNWR). President Theodore Roosevelt established the MNWR in 1908 because the lake system was one of the largest freshwater marshes in the United States and serves as an important stop and breeding ground along the Pacific Flyway for millions of migratory birds. The refuge is managed by the U.S. Fish and Wildlife Service.
Since the 1990s, Malheur Lake - which averages depths of about 1 meter - has been in a degraded, turbid state, which is characterized by a lack of vegetation, high turbidity, and high algae content. Multiple factors may have contributed to the shift from a clear to turbid state. For example, the introduction of non-native common carp in the 1920s negatively impacted lake vegetation and clarity. Environmental events such as multiple years of flooding in the 1980s and changes in land use and climate may have also affected lake water quality.
USGS research:
USGS scientists are part of an ongoing effort to identify the processes that maintain the turbid state at Malheur Lake and to determine the threshold that must be achieved through restoration activities to return the lake to its clear, vegetated state. Studies have investigated the physical characteristics of suspended material in the lake, the sources of suspended sediment (such as tributary inputs), solar radiation through the water column, and the erodibility of the lakebed. In addition, researchers have investigated factors that influence the concentration of suspended material such as water depth, nutrient concentrations, wind speed, and precipitation.
Major findings include:
- High suspended-sediment concentrations within Malheur Lake likely are negatively affecting the survival of desirable aquatic plants.
- Lakebed and suspended sediments are mostly very fine-grained material (less than 63 micrometers) that limit sunlight available for plants.
- Wind speeds above 11–22 miles per hour (5–10 meters per second) resuspend lakebed material causing rapid increases in turbidity that can last for several days, which occurs frequently.
- Between wind events, turbidity values remain at a persistent baseline level.
- Land-use practices and water diversions along tributaries affect the water quantity and the nutrient and suspended-sediment concentrations reaching the lake.
- In 2019 (a wet water year), approximately two-thirds of the increase in suspended-sediment storage in the water column was attributed to internal resuspension and one-third was from external loading.
- The internal resuspension, deposition, and external loading of suspended sediment likely is decreasing lakebed variability.
- Total phosphorus and orthophosphate concentrations measured over the past 5 years are substantially higher than in the 1980s, and the lake is eutrophic.
- Water availability and water management affect the types and quantity of bird habitat throughout the Malheur National Wildlife Refuge during irrigation months.
- The relation between the amount of bird habitat and the extent (partial and open water) of Malheur Lake varies by bird guild.
- The Donner und Blitzen River supplied all or most of the surface water inflow to Malheur Lake during the analysis years (April 2021 – July 2024), emphasizing the importance of informed management of the river.
- In dry water years with low snowpack and streamflow, resource managers could optimize the amount of habitat for specific bird guilds using the Water for Birds Tool.
Future lake management and restoration aim to reestablish vegetation and reduce suspended material in the water column to increase the amount and quality of food resources for birds. Restoration actions could target wind-driven turbidity events by planting bulrush to create a natural wave reduction barrier. For baseline turbidity levels, adding a coagulant, like alum and bentonite clay, could be used to clump up suspended material so it sinks to the bottom and improves water clarity. Restoration actions that prioritize vegetation establishment would reduce bioavailable nutrients for phytoplankton while increasing light in the water column.
Media
Sources/Usage: Public Domain. View Media Details
USGS research informs restoration efforts:
Based on these findings, a mesocosm study was designed by the USGS. In 2021 and 2023, mesocosms were constructed in the lake to test ways to reduce suspended sediment in the water to promote plant growth. Mesocosm treatments included 1) wind barriers to reduce wave action that stirs up sediment, 2) flocculating suspended materials so that it sinks to the bottom, 3) the addition of sand to harden the lakebed, and 4) combinations of those treatments. All of the treatments used in this study could be scalable to try and restore portions of the lake in the future.
Results from mesocosm study:
- Flocculation temporarily decreased turbidity by ≥ 90% and significantly increased photosynthetically active radiation by > 400% through the water column.
- Wave-reduction barriers did not affect suspended sediment concentrations or light infiltration because of the variable wind directions at the study site.
- The light required for submerged aquatic vegetation can be temporarily attained at the lakebed using flocculation, but future experiments could attempt to prolong the duration of low turbidity by effectively capping the flocculated material.
Media
Sources/Usage: Public Domain. View Media Details
Related science project web pages.
Water Quality
The USGS, in partnership with multiple other groups, is learning about water-quality conditions across time and space in terminal lakes across the Great Basin. This effort is part of the Saline Lake Ecosystems Integrated Water Availability Assessment.
Bulrush growing in Malheur Lake
Following a wet winter, bulrush is shown growing in Malheur Lake. Emergent vegetation like bulrush provides nesting habitat and food resources for birds.
Applying sand to Malheur Lake mesocosm
Local sand was applied to some mesocosms to test whether hardening the lakebed would reduce suspension of bottom sediments.
Local sand was applied to some mesocosms to test whether hardening the lakebed would reduce suspension of bottom sediments.
USGS scientists have partnered with local groups to learn about the processes affecting turbidity in Malheur Lake. Located in southeastern Oregon, Malheur Lake and the surrounding refuge provide critical habitat to birds migrating along the Pacific Flyway.
Media
Sources/Usage: Public Domain. View Media Details
Overview:
Malheur Lake is the largest lake in the Harney Basin in southeastern Oregon and is located within the Malheur National Wildlife Refuge (MNWR). President Theodore Roosevelt established the MNWR in 1908 because the lake system was one of the largest freshwater marshes in the United States and serves as an important stop and breeding ground along the Pacific Flyway for millions of migratory birds. The refuge is managed by the U.S. Fish and Wildlife Service.
Since the 1990s, Malheur Lake - which averages depths of about 1 meter - has been in a degraded, turbid state, which is characterized by a lack of vegetation, high turbidity, and high algae content. Multiple factors may have contributed to the shift from a clear to turbid state. For example, the introduction of non-native common carp in the 1920s negatively impacted lake vegetation and clarity. Environmental events such as multiple years of flooding in the 1980s and changes in land use and climate may have also affected lake water quality.
USGS research:
USGS scientists are part of an ongoing effort to identify the processes that maintain the turbid state at Malheur Lake and to determine the threshold that must be achieved through restoration activities to return the lake to its clear, vegetated state. Studies have investigated the physical characteristics of suspended material in the lake, the sources of suspended sediment (such as tributary inputs), solar radiation through the water column, and the erodibility of the lakebed. In addition, researchers have investigated factors that influence the concentration of suspended material such as water depth, nutrient concentrations, wind speed, and precipitation.
Major findings include:
- High suspended-sediment concentrations within Malheur Lake likely are negatively affecting the survival of desirable aquatic plants.
- Lakebed and suspended sediments are mostly very fine-grained material (less than 63 micrometers) that limit sunlight available for plants.
- Wind speeds above 11–22 miles per hour (5–10 meters per second) resuspend lakebed material causing rapid increases in turbidity that can last for several days, which occurs frequently.
- Between wind events, turbidity values remain at a persistent baseline level.
- Land-use practices and water diversions along tributaries affect the water quantity and the nutrient and suspended-sediment concentrations reaching the lake.
- In 2019 (a wet water year), approximately two-thirds of the increase in suspended-sediment storage in the water column was attributed to internal resuspension and one-third was from external loading.
- The internal resuspension, deposition, and external loading of suspended sediment likely is decreasing lakebed variability.
- Total phosphorus and orthophosphate concentrations measured over the past 5 years are substantially higher than in the 1980s, and the lake is eutrophic.
- Water availability and water management affect the types and quantity of bird habitat throughout the Malheur National Wildlife Refuge during irrigation months.
- The relation between the amount of bird habitat and the extent (partial and open water) of Malheur Lake varies by bird guild.
- The Donner und Blitzen River supplied all or most of the surface water inflow to Malheur Lake during the analysis years (April 2021 – July 2024), emphasizing the importance of informed management of the river.
- In dry water years with low snowpack and streamflow, resource managers could optimize the amount of habitat for specific bird guilds using the Water for Birds Tool.
Future lake management and restoration aim to reestablish vegetation and reduce suspended material in the water column to increase the amount and quality of food resources for birds. Restoration actions could target wind-driven turbidity events by planting bulrush to create a natural wave reduction barrier. For baseline turbidity levels, adding a coagulant, like alum and bentonite clay, could be used to clump up suspended material so it sinks to the bottom and improves water clarity. Restoration actions that prioritize vegetation establishment would reduce bioavailable nutrients for phytoplankton while increasing light in the water column.
Media
Sources/Usage: Public Domain. View Media Details
USGS research informs restoration efforts:
Based on these findings, a mesocosm study was designed by the USGS. In 2021 and 2023, mesocosms were constructed in the lake to test ways to reduce suspended sediment in the water to promote plant growth. Mesocosm treatments included 1) wind barriers to reduce wave action that stirs up sediment, 2) flocculating suspended materials so that it sinks to the bottom, 3) the addition of sand to harden the lakebed, and 4) combinations of those treatments. All of the treatments used in this study could be scalable to try and restore portions of the lake in the future.
Results from mesocosm study:
- Flocculation temporarily decreased turbidity by ≥ 90% and significantly increased photosynthetically active radiation by > 400% through the water column.
- Wave-reduction barriers did not affect suspended sediment concentrations or light infiltration because of the variable wind directions at the study site.
- The light required for submerged aquatic vegetation can be temporarily attained at the lakebed using flocculation, but future experiments could attempt to prolong the duration of low turbidity by effectively capping the flocculated material.
Media
Sources/Usage: Public Domain. View Media Details
Related science project web pages.
Water Quality
The USGS, in partnership with multiple other groups, is learning about water-quality conditions across time and space in terminal lakes across the Great Basin. This effort is part of the Saline Lake Ecosystems Integrated Water Availability Assessment.
Bulrush growing in Malheur Lake
Following a wet winter, bulrush is shown growing in Malheur Lake. Emergent vegetation like bulrush provides nesting habitat and food resources for birds.
Following a wet winter, bulrush is shown growing in Malheur Lake. Emergent vegetation like bulrush provides nesting habitat and food resources for birds.
Applying sand to Malheur Lake mesocosm
Local sand was applied to some mesocosms to test whether hardening the lakebed would reduce suspension of bottom sediments.
Local sand was applied to some mesocosms to test whether hardening the lakebed would reduce suspension of bottom sediments.