Tracking Change in the Upper Deschutes: What We’re Learning About River Health

The 2024 Upper Deschutes River Mitigation and Enhancement (M&E)Annual Report offers a look at how aquatic ecosystems in the Deschutes River basin are responding to evolving water management practices and restoration efforts. Ben Stout, the Oregon Department of Fish and Wildlife M&E Coordinator for the Deschutes Watershed District, reported on multiple indicators used to track the ecological health across the river system.

Why the Report Matters

The Mitigation and Enhancement (M&E) program, funded by the Central Oregon Irrigation District (COID), was created in the 1980s to help mitigate or offset impacts to the Upper Deschutes River from the COID SiphonHydroelectric Project. The M&E Coordinator's evolving role now centers on monitoring river health—particularly fish populations, habitat conditions, macro-invertebrates, and water quality—to gauge the effects of conservation measures that increase streamflow under the Deschutes Basin Habitat Conservation Plan (DBHCP) as well as ongoing flow restoration efforts in the middle Deschutes.

Historic Challenges and the Need for Change

The upper Deschutes River, historically stable and ranging between 600-800 cfs year-round due to spring-fed flows, now endures a highly altered hydrograph. In winter, altered flows dipped to as low as 20 cfs due to water storage behind Crane Prairie and Wickiup Reservoirs—built in 1922 and 1949, respectively. Now, minimum winter flows are set to a minimum of 100 cfs. This seasonal drying dewaters critical habitat, causes bank erosion when flows increase in the spring and summer to deliver irrigation water, and impacts spawning grounds for native fish and wetlands for Oregon spotted frog.

In response, the DBHCP outlines gradual increases in minimum winter flows below Wickiup Dam, targeting 100 cfs in early years and eventually reaching 400-500 cfs by 2050. These measures aim to reverse some of the ecological degradation caused by earlier practices.

Redband Trout: A Closer Look

Redband trout are a native subspecies of rainbow trout and are well-adapted to the high desert conditions in Central Oregon. Since 2018,ODFW has been electrofishing 8 kilometers (km) of a 14-km stretch of theDeschutes River just downstream of Wickiup Dam every fall to monitor fish populations.

Here’s what the 2024 data shows about redband trout:

• Population Structure: The number of redband trout captured in 2024 was similar to recent years, but the fish were generally smaller. The average length was 8 ½ inches, which is a bit shorter than in earlier years of the study.
• Fish  Condition: While the trout may be smaller, their overall condition has improved. Researchers use a metric called Fulton’s K factor to measure this—it essentially tells you if a fish is underweight or in good shape for its size. In 2024, redband trout had a K factor of 1.14, which is considered healthy and an increase from 1.07 in 2022 and 1.12 in 2023.
• Fewer Large Fish: One noticeable trend is that very few redband trout larger than 19 ½ inches were captured in 2023 or 2024. That doesn’t necessarily mean they’re not present, but it does suggest that fewer fish are reaching older, larger age classes.

So, while the fish might be smaller than in past years, their improved condition is encouraging. It could suggest better food availability, better overwintering habitat, or less stress overall—though more monitoring will be needed to understand what’s driving this change.

Brown Trout

Brown trout continued to dominate, with 2024 showing a strong presence of younger age classes. Average lengths were lower than in past years due to this influx of juveniles, but the fish were in fair condition.Fulton’s K factor rose from 0.99 in 2022 to 1.09 in 2024.

Mountain Whitefish

Whitefish populations appeared steady, with signs of stronger age-2 classes in 2023 and 2024. While their condition declined compared to earlier years, it remained consistent over the past two.

Kokanee

Kokanee, another non-native species, were largely absent from recent samples, suggesting a decrease in the number of fish lost or entrained from Wickiup Reservoir when reservoir storage is not reduced below approximately 10% of the overall storage capacity. Early years of DBHCP implementation coincided with drought and Wickiup Reservoir was drained down to the relict stream channel resulting in thousands of kokanee and other reservoir fish to be flushed into the Upper Deschutes River.

Spawning Ground Surveys: Mixed Results

Spawning surveys for redband and brown trout were conducted in the Deschutes River and Fall River using raft-mounted observation platforms and pedestrian surveys. Results showed fluctuating redd (spawning nest) counts year-to-year.

In 2024, redband trout redds showed a slight increase in the reach below Wickiup Dam but decreased downstream.  Brown trout redd counts dropped from a 2023 peak but remained higher than in 2022. Fall River redd counts for both species trended downward overall. These fluctuations are influenced by water flow, temperature, habitat availability, and egg survival conditions.

Macro-invertebrates: Vital Indicators of River Health

Macro-invertebrates are sensitive indicators of ecological change. Since 2021, samples have been collected at sites from Wickiup Dam toSteelhead Falls and in tributaries like Fall River, Little Deschutes, and Tumalo Creek. These benthic organisms help assess watershed health, pollution levels, and food availability for fish.

Although results from 2023 and 2024 are pending due to funding needs, early data from 2021 and 2022 suggest meaningful baseline trends are forming. Continued sampling will help evaluate how new flow regimes affect the broader aquatic food web.

Juvenile Trout: A Window into the River’s Future

To assess trout recruitment, three-pass electro fishing surveys were conducted along river margins of the middle Deschutes—targeting young-of-the-year (YOY) trout. In 2024, estimates ranged from 106 to nearly3,000 trout per river mile per bank. Brown trout juveniles were generally larger than redband, likely due to earlier spawning and growth.

High-producing areas like Foley Waters and Steelhead Falls were consistent across years, providing critical rearing habitat. Monitoring YOY trout allows managers to detect subtle ecological shifts and prioritize conservation in key habitats.

Surface Water Temperatures: Climate and ManagementCollide

Water temperature is a major stressor for cold-water fish species. Using data loggers, ODFW and partners tracked hourly temperatures across 12 mainstem and tributary sites during the warmest months.

Spring-fed streams like Fall and Spring Rivers remained cool (<60°F), likely due to spring inflows bringing in more water and cooler temperatures. However, the Little Deschutes and downstream sites like Odin andCline Falls peaked over 76°F—above the preferred temperature range for redband trout (68°F), mountain whitefish (63°F), and bull trout (54°F). These temperature spikes result from both hot weather and drastically reduced flows below theNorth Canal Dam during irrigation season, leaving the river vulnerable to warming.

Fish Passage: A Success Story at North Canal Dam

Installed in 2017, the North Canal Dam fish ladder was monitored using passive integrated transponder (PIT) tag technology from 2018 through 2023. Over 500 fish were tagged, and results show effective passage for multiple species, a rare success. With no new trends in 2024, tagging was suspended, and antenna removal is planned.

Expanding the Scope: New Directions in 2025

The 2025 work plan includes all ongoing monitoring efforts and several new initiatives, funded in part by an Oregon Watershed Enhancement Board grant. These include:

• Trout abundance estimates using mark-recapture
• Age and growth studies via scale collection
• Seasonal fish use of off-channel habitats
• Macro-invertebrate and temperature monitoring in these habitats

These expanded efforts reflect a holistic approach to understanding river dynamics, especially as flow restoration measures continue to unfold.

Conclusion

The 2024 M&E Report for the Upper Deschutes River paints a cautiously optimistic picture. While fish populations show signs of resilience and improvement, challenges like high temperatures, altered flows, and habitat limitations persist. As the river adjusts to new flow management practices, continued monitoring and adaptive management will be essential to securing a healthier future for the river’s native fish and the broader ecosystem they support.

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