Save Wild Trout Releases First-of-its-Kind Scientific Reports on Jefferson Basin

Written By Quincey Johnson

Most Comprehensive Study Highlights Threats to Southwest Montana’s Cold Water Rivers and Wild Trout

(HELENA, MT) – Yesterday evening, Save Wild Trout released the most comprehensive scientific report to date on water quality in the Jefferson River Basin at a public event online and in Helena.

The primary report, “Jefferson River Basin Abiotic Monitoring 2023-2024,” is the result of a multi-year study integrating drone-based thermal (FLIR) imaging, in-stream water quality sampling, and extensive on-the-ground monitoring. Released alongside it was a companion report, Thermal Refugia Mapping in the Jefferson Basin Using FLIR Technology, which presents findings from a first-of-its-kind drone-based Forward-Looking Infrared (FLIR) survey. Together, the reports identify key environmental stressors affecting cold water habitat in the Jefferson Basin, such as nutrient pollution, reduced dissolved oxygen, warming water temperatures, and increasing algal growth. 

“Water-quality monitoring conducted by Save Wild Trout in the Jefferson River basin during 2023 and 2024 identified notable patterns of thermal and oxygen-related stress in three of the four rivers evaluated. Free-flowing systems, including the Big Hole and Jefferson rivers, exhibited widespread impacts with water temperature and dissolved oxygen exceeding thresholds suitable for juvenile or adult salmonids at multiple locations. Conversely, tailwater systems like the upper Beaverhead and Ruby rivers benefited from cold-water releases at dams, which helped regulate water temperatures and maintain dissolved oxygen levels in proximity to the reservoir for part of the summer,” said Dr Kyle Flynn, Lead Scientist for Save Wild Trout. “Findings from Save Wild Trout's monitoring campaign highlight the need for targeted, site-specific management strategies within the Jefferson River Basin to restore and protect cold-water fisheries and wild trout.”

Key findings from the report include:

  1. Beneficial uses of three of the four rivers monitored by SWT in 2023 and 2024 are impaired. This includes the lower Beaverhead, upper and lower Big Hole, and Jefferson rivers, all of which experienced harmful thermal and DO water-quality conditions that are injurious to aquatic life.

  2. Thermal buffering by reservoir releases provide essential refugia for trout during peak heat periods. However, downstream sections, particularly those influenced by water withdrawals and nutrient inputs, may be impaired due to compounded stress from temperature, low DO, and elevated primary productivity.

  3. Site-specific management actions across the Jefferson River Basin to restore and sustain cold-water fisheries are needed, along with continued data collection and analysis. Potential mitigation actions include flow enhancement or conservation, riparian shade improvement, and reducing nutrient inputs.

The event also addressed recent observations of widespread algal blooms in the Jefferson River Basin, with drone footage documenting significant algae growth in late June on the Jefferson, Big Hole, and Boulder Rivers. Two fish exhibiting signs of head necrosis were also reported and submitted to Montana Fish, Wildlife & Parks and the Department of Environmental Quality. Save Wild Trout Director Brian Wheeler also documented algae on July 12th and 13th throughout the Jefferson Basin. 

“The early appearance of these algal blooms should be a wake-up call,” said Brian Wheeler, Save Wild Trout’s Program Director. “Early season algal blooms are indicative of real water quality issues tied to nutrient pollution and warming waters. Now is the time to use science to take action to protect Montana’s cold-water fisheries.”

The reports, event recording, and a Frequently Asked Questions (FAQ) document are available here: 

Quincey Johnson
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FAQ: Save Wild Trout Abiotic FY23/24 Report