For over 40 years, the U.S. Forest Service has been monitoring high-altitude mountain lakes in Colorado to track the environmental impacts of human-caused pollutants and climate changes in delicate wilderness areas and ecosystems. 

Mountain lakes are extremely sensitive, making them a perfect testing ground for measuring ecosystem changes in climate and the environment. 

Mary Jade Farruggia, a postdoctoral researcher at the University of Colorado Boulder’s mountain limnology lab, described them as a “canary in the coal mine” or an early warning system that can help guide which larger ecosystem changes researchers need to look out for. 

“They often show changes as a result of the environment early on, before less sensitive ecosystems might,” Farruggia said. “Understanding how the most sensitive ecosystem changes as a result of our changing environmental conditions provides important foresight for how less sensitive ecosystems may change in the future.”

Farruggia recently partnered with researchers from the Forest Service and University of Colorado Boulder to look at data from 35 southern Rocky Mountain lakes collected as part of the federal agency’s long-term air monitoring program. The study set out to determine whether environmental changes — including climate change and air pollution — have impacted the lakes’ chemistry and ecosystem over time. 

The program and samples collected support various federal efforts — including the National Atmospheric Deposition Program and the Interagency Monitoring of Protected Visual Environments program — created following the 1977 Clean Air Act to assess air and water quality in sensitive, high-elevation wilderness areas. 

Over the last 40 years, over 2,500 samples have been collected in these 35 lakes ranging from 9,600 feet of elevation to 13,000 feet, Farruggia said. All but two lakes, located in the Wind River Range in west central Wyoming, are in Colorado. They span six national forests, 11 wilderness areas and 14 ranger districts. 

Typically, samples are collected from each lake two times every summer. In the past, occasional samples were taken in the winter. With recent changes, Farruggia said the samples look at 19 different chemical parameters, an increase from the 13 it has historically tested for. 

This type of “large-scale, long-term monitoring” is extremely valuable, “particularly as our climate becomes more variable and extreme,” Farruggia said. 

“We cannot measure just one or two mountain lakes for a year or two and extrapolate to all other mountain lakes over decades. We need large programs like this one to capture the variability in lake responses to change over both space and time,” she added. 

According to Farruggia, this type of monitoring and data could help answer questions about how this winter’s historically low snowpack in Colorado could impact mountain lakes. 

“For example, we found that some lakes in this dataset are strongly influenced by precipitation, and will be especially sensitive to an extreme snowpack, meaning they will likely experience more change as a result of an extreme snowpack,” she said. “Insights like this can help natural resource managers understand which ecosystems may be most at risk and adapt their management for a changing climate.”

Many of these samples are collected by volunteers and nonprofits. In the Roaring Fork Valley and White River National Forest, Wilderness Workshop, a Carbondale-based conservation nonprofit, has supported the data collection since the late 1980s. The nonprofit has partnered with the national forest to fund a technician position that collects samples in 15 regional lakes. 

“These wilderness and high-mountain lake datasets represent some of the longest-term observations we have for these sensitive ecosystems across the central Rockies,” said Will Roush, executive director of the Wilderness Workshop. “These are the nation’s headwaters, everything else, across dozens of states, is downstream. The long-term monitoring of air and water quality provides a baseline we can use to understand the status of these lake resources and changes that could impact the health of people, wildlife and ecosystems.” 

Last year, after federal budget cuts hit the program, Pitkin County’s Healthy Rivers and Streams Program stepped up to fund and support the White River work in 2026. However, Roush warned that “federal funding is critical for the long-term continuation of the program.”

What is driving changes in mountain lake chemistry? 

In a February webinar, Farruggia presented results from their study of the dataset. Isabella Oleksy, also with the University of Colorado Boulder’s mountain limnology lab, and Tim Fegel and Chuck Rhoades, with the U.S. Forest Service’s Rocky Mountain Research Station contributed to the study. 

“We went into it knowing that high elevation lakes such as these tend to be especially susceptible to environmental change due to their clear, dilute waters, small watersheds and sparse vegetation,” she said. “We didn’t know exactly if/how environmental change would affect the lakes, and how sensitive they might be.”

Specifically, the study set out to evaluate how changes in pollutants and emissions, drought conditions and warmer temperatures impacted levels of nitrogen and sulfate in the lakes. 

“Air pollution is the major source of nitrogen and sulfate in these systems,” Farruggia said. “Both nitrogen and sulfate contribute significantly to a lake’s acidity … An acidic lake can harm fish and wildlife, change the chemistry of the lake enough to promote reactions that release toxic metals into the water and make lakes less able to resist further additions of acid.” 

Both chemicals can travel long distances before depositing into these high-elevation lakes. 

Nitrogren, specifically, acts as a “MiracleGro” for lake algae, she added. 

“Lots of nitrogen can promote algal blooms, turning lakes green and less clear,” Farruggia said. “This is exacerbated by warming summer air temperatures due to climate change, since algae also grow better and faster in warmer temperatures.”

As the study set out to determine whether regional trends in air pollution or climate were impacting sulfate and nitrogen levels, they determined that these trends only served as an explanation for sulfate levels in around half the lakes and nitrogen levels in around 30% of the lakes, Farruggia said. 

While most lakes have experienced chemical changes in the past 40 years captured by the dataset, the magnitude and direction of the changes varied at each individual lake. Farruggia described it as “mosaic of regional to local factors” — erosion, drought, land cover, geography, size, elevation and more — that are all interacting to shape the chemical trends and changes at each location. 

“It’s clear that climate and or deposition matter to some lakes, but there isn’t one like golden variable that explains everything about how and why lake chemistry is changing,” Farruggia said. “It’s not quite as simple as being like, we’ve improved air pollution, and therefore, we’ve improved the same pollutants in lakes, unfortunately. So, we’ve just seen that it’s likely a combination of several factors driving change in these lakes.”

While the study is continuing to determine whether more “static” variables like soil and geology interact with pollution and climate, and how they impact levels of sulfate and nitrogen, Farruggia said the results really punctuate the need for this type of widespread, long-term monitoring.   

“Given that our future is not projected to be stationary, climate is projected to become more variable, more extreme,” she said. “We really need this continued monitoring for determining lake responses to ongoing change. We see that most of these relationships are not linear, a lot of them are squiggly.”