Scientific Research

Programs Overview        Education and Outreach       Community Stewardship

WLI conducts scientific research for the community and resource managers to enable them to make informed decisions in the Whitefish Lake Watershed and beyond.


The Science Advisory Committee (SAC) provides scientific and technical guidance to WLI, focusing on WLI's efforts to conduct research that results in useful data for the community and resource management decision makers in the Whitefish Lake Watershed and beyond. See who is on the Science Advisory Committee.

WLI has developed data collection parameters, obtained data collection equipment, and increased the level of scientific research on Whitefish Lake, its tributaries and local area steams. Because most pollutants and water chemistry changes are invisible to the naked eye, one cannot evaluate water quality solely by visual inspection. Similarly, because water chemistries and conditions change seasonally and annually, one cannot understand overall lake dynamics by monitoring it for a year or two. It requires that specific measurements be evaluated in respect to one another over time to gain a holistic understanding of the resource.

WLI has typically been collecting baseline data at two permanent sites on Whitefish Lake and on its tributaries since 2007. Data collection typically starts in April and runs through November. Data is collected on all of the lake's tributaries; Hellroaring Creek, Lazy Creek, Smith Creek, Swift Creek, Beaver Creek and Viking Creek, as well as local streams Cow Creek, Haskill Creek, Walker Creek, and the Whitefish River. WLI also conducts annual sampling of Whitefish Lake for Aquatic Invasive Species (AIS) such as Eurasian watermilfoil, zebra and quagga mussels. See AIS page for more information.

WLI and partner data are available in the Whitefish Water Resources Report: A Status of the Whitefish Lake Watershed and Surrounding Area.

WLI installed and maintains a Weather Station near Lazy Bay from which we collect wet and dry precipitation and other atmospheric data.


WLI takes on special projects based on the recommendations of the community and the need for scientific information. Since 2005, we have conducted research for special projects on Whitefish Lake, Tally Lake, Swan Lake, and Blanchard Lake. This work is typically funded by research grants or through programmatic partnerships.

Here are some of our past special projects:

Investigation of Septic Leachate to the Shoreline Area of Whitefish Lake

In 2011, we conducted the Investigation of Septic Leachate to the Shoreline Areas of Whitefish Lake. In this study, we used a number of parameters including fluorometry, E. coli, and DNA testing, to research potential septic leachate contamination to the littoral (shoreline) areas of Whitefish Lake. The results of this study were made available in early 2012.

In 2013, the City of Whitefish formed the ad hoc Whitefish Community Wastewater Committee (WCWC) to develop management options for addressing the septic leachate issues identifies in the WLI study. WLI's executive director and science and education director were tapped as technical facilitators to the committee. The WCWC delivered the Whitefish Community Wastewater Management Program to City Council which approved its implementation through the resolution process. Through this program, two studies were conducted resulting in neighborhood-focused Preliminary Engineering Reports (PER). WLI and the City will be addressing the septic leachate issue for many years. Get an update here: (See Whitefish Lake Institute Report Downloads - Septic Leachate Issue: Support Documents).

Link to report

Biological Communities Research
As described in WLI’s Whitefish Water Resources Report: A Status of the Whitefish Lake Watershed and Surrounding Area, Whitefish Lake is oligo-mesotrophic, meaning its water quality can easily be influenced toward decline.  Of the many factors that influence water quality, the trophic structure of the lake has received little attention. WLI has begun conducting research on the biological communities of the lake in an effort to better understand that trophic structure.

In 2013, WLI conducted a 395 point macrophyte and substrate survey along the Whitefish Lake shoreline The survey consisted of determining the composition and relative abundance of plant species at each location, along with characterizing the lake substrate to determine areas suitable for plant colonization. No exotic invasive species were found. Six additional lakes were chosen for macrophyte surveys and early AIS detection in 2014. Lakes were chosen based on proximity to Whitefish Lake and include: Blanchard, Dollar, Lost Coon, Murray, Skyles and Spencer. Lakes were sampled within the first eight days of September. The survey consisted of determining the composition and relative abundance of plant species at each lake along with characterizing the lake substrate to determine areas suitable for plant colonization. Additional surveys have been conducted by WLI for early detection monitoring of Eurasian watermilfoil (EWM) at many locations including Beaver Bay, Lazy Bay, State Park, the outfall of Viking Creek and City Beach. No EWM was discovered during the surveys, however, additional surveying will continue based on suitable areas for colonization, recreational pressure, and proximity to Beaver Lake which does have EWM. Results of these studies can be found in the Whitefish Water Resources Report: A Status of the Whitefish Lake Watershed and Surrounding Area.

Aquatic Macroinvertebrates were sampled by WLI and analyzed by Rithron Associates in 2015 to determine community assemblages and their relative pollutant tolerance. WLI sampled Whitefish Lake as well as its tributaries including the East Fork of Swift Creek, West Fork of Swift Creek, Swift Creek Mainstem, Lazy Creek, Hellroaring Creek, Beaver Creek, Viking Creek, Upper Whitefish River, Cow Creek, Haskill Creek, and Walker Creek. Macroinvertebrates such as insects, worms, mussels, and snails, tend to be sensitive—in varying degrees— to pollutants. When found in large numbers, macroinvertebrates that require high dissolved oxygen levels tend to indicate good water quality. Because many macroinvertebrate community assemblages change with declining water quality, they are good indicators of negatively impacted water quality. Existing populations can also elucidate specific aquatic ecosystem changes such as increases in sediment and thermal pollution. Sampling and identifying macroinvertebrate life allows researchers to set a baseline of water quality from which to measure any changes. Thanks to funding from the Cadeau Foundation, WLI now has a professionally conducted baseline macroinvertebrate study that helps describe the health of Whitefish Lake tributaries, Whitefish Lake, and Whitefish Lake Watershed streams. This information will also be used to compare future research results, allowing WLI to report changes from outside influences such as development, pollutants, and climate. Results from this baseline survey can be found in the Whitefish Water Resources Report: A Status of the Whitefish Lake Watershed and Surrounding Area.

Mysis Shrimp
Mysis shrimp (Mysis diluviana) are a nonnative species introduced to Whitefish Lake in 1968, and a species of concern regarding the trophic status of the lake. Mysis have had significant adverse impacts on the Flathead Lake ecosystem, so it is important that we assess their population densities and distribution locally. This Mysis study will be compared to prior studies in the 1980s to provide a necessary update regarding the trophic status and dynamics of Whitefish Lake. Results will inform management activities on the relationship to fish populations and nutrient cycling to understand food web dynamics for recreational angling, and for the overall economic benefit of the lake to the community. Mysis shrimp have been described as the most deterministic event in the legacy of Flathead Lake and the Flathead Basin. Mysis introductions were expected to provide a food source for benthic-feeding fishes such as lake trout, and for pelagic planktivores such as kokanee salmon. However it was later discovered that the expected increased forage for kokanee salmon from the Mysis shrimp transplant was based on erroneous interpretations of the results of introductions elsewhere.

WCF_Logo The Whitefish Community Foundation funded a 2016 Mysis shrimp study which took place in early September during the low light phase of the lunar cycle. Sampling occurred after midnight when Mysis shrimp have migrated from the lake bottom vertically to the near surface. Additional information about Mysis shrimp can be found in the Whitefish Water Resources Report: A Status of the Whitefish Lake Watershed and Surrounding Area.

Periphyton is a complex mix of algae, cyanobacteria, microbes, and detritus that is attached to submerged surfaces in aquatic ecosystems. Like macroinvertebrates, periphyton is an important water quality indicator because it is sensitive to and responds quickly to change, and is fairly easy to sample. Periphyton has long been used as a water quality indicator in lotic systems (streams and rivers), but no metrics have yet been developed for determining periphyton tolerance in lentic systems (freshwater lakes). This study will not only provide a needed benchmark for the Whitefish Lake Watershed, but will also have a multiplier effect, furthering science through the development of periphyton analysis for other lakes in the northwest Montana region. Understanding periphyton will further WLI’s knowledge of and ability to manage the waterbodies of the Whitefish Lake Watershed and provide aquatic resource managers with a new management tool. Thanks to funding provided by the Cadeau Foundation, WLI has baseline periphytom information for a better description of the health of Whitefish Lake.

Rangewide Bull Trout eDNA Study
WLI is excited to be participating in the Rangewide Bull Trout eDNA Study in the Whitefish Lake Watershed. Environmental DNA (eDNA) refers to fragments of genetic material from plants or animals that naturally occur in the environment. In the case of fish, DNA is contained in cells that are continually shed into the water, thus becoming “eDNA.” Each species DNA is unique and can be detected in very small quantities. Scientists can now quickly confirm if a certain species is present in a stream by filtering the water and using laboratory analysis to look for its unique DNA.

Though once abundant, Montana’s native bull trout have declined in many locations and are at risk from a changing climate, non-native species competition, and habitat degradation. The Rangewide Bull Trout eDNA Study is determining the distribution of bull trout throughout the Pacific Northwest. Thanks to this funding, WLI is one of many organizations contributing to this effort.

eDNA sampling is a relatively new, exciting tool with high cost-effectiveness in determining population structure and answering other questions. WLI has utilized eDNA technology since 2013 as it relates to determining presence/absence of aquatic invasive species, now an increased threat in the Watershed. This technology is constantly being refined to facilitate sound management of our aquatic resources.

Gasoline Constituent Loading and Motorized Watercraft Use Levels in Whitefish Lake
This 2005 study examined potential public health risk from motorized watercraft-caused gasoline constituent loading to shoreline areas used for recreation. WLI analyzed the levels of BTEX (benzene, ethylbenzene, toluene and xylene), agents known to cause myriad health problems from cancer and birth defects to nervous system, liver and kidney damage. Results found high levels of benzene at City Beach. WLI concluded that the main mechanism for the high levels of benzene was when a boat owner pulls their transom plug on the boat ramp, petroleum effluent enters the lake adjacent to the swimming area. WLI recommended the installation of a catchment system to collect the effluent. The Whitefish City Council approved financing for the project which was completed in 2013.

Lake Usage Data
WLI developed and completed a survey detailing how the children of Whitefish use Whitefish Lake as a recreational resource. WLI surveyed children in grades 4, 8, and 11. With the support of Whitefish Public Schools, WLI achieved a 90% respondent rate of total enrollment. The survey found that 89% of respondents recreated in the lake that year. While fishing was not of great interest to the kids, 87% of them swam in the lake. Of the 87%, 29% claim to have swam twenty days or more. This social survey provided additional data to support the installation of the grate/catchment system at City Beach.

Tally Lake
Tally Lake is the second deepest lake in Montana and regionally unique due to its morphometric (size and shape) attributes and chemical input (humic matter) from Star Meadows. Those factors, among others, lead to a severe depletion of dissolved oxygen at depth throughout the calendar year. WLI is the first to monitor Tally Lake from the surface to bottom (445 feet). In 2008, a preliminary study was funded by Montana Department of Environmental Quality (DEQ). From 2009 to 2013 work continued via a US Forest Service Resource Advisory Committee grants. From 2014 through the present, research on Tally Lake has been supported by WLI members.

click to view the Tally Lake
3-D animation

Swan Lake
WLI conducted sampling on Swan Lake for the Montana Department of Environmental Quality in 2009. WLI also donated time to collect Hydrolab data and submitted that data to the Swan Ecosystem Center. Work continued from 2010 through 2013 via a combination of contracts with the Swan Lakers, Kootenai Lodge Estates and the Swan Ecosystem Center. WLI has provided a summary report and has presented information at two Swan Lakers Annual Meetings. WLI presented information at two Swan Lakers Annual Meetings, and the 2014 final project report is available here.

Link to report

Blanchard Lake
Blanchard Lake is a warm water lake located about 2 miles south of Whitefish. The lake has relatively shallow depths, and no inflow or outflow of fresh water. Blanchard is broadly vegetated and supports several warm water fish and other aquatic species. WLI maintains two monitoring sites on the lake, where water quality monitoring parameters are collected using a Hydrolab DS5 Sonde. Water chemistry samples are also collected once annually as part of the NWMTLVMN program. Reporting on lake water quality is made to the Friends of Blanchard Lake, a group dedicated to protecting the water quality and natural resources of the lake and its surrounding area.

Bigfork Stormwater Project
WLI provided technical assistance to Flathead County and the Bigfork Storm Water Advisory Committee during the Bigfork Storm Water Project. WLI developed and implemented a Sample and Analysis Plan to collect water quality samples before and after storm water infrastructure and treatment devices were installed. WLI presented findings at the 2012 Montana Stormwater Conference, and the 2014 final project report is available here.

The Northwest Montana Lakes Volunteer Monitoring Network (NWMTLVMN) is a citizen science program that grew out of two monitoring programs previously underway at the Flathead Basin Commission (FBC) and the Whitefish Lake Institute (WLI). The Flathead Basin Commission, in cooperation with the University of Montana Flathead Lake Biological Station, coordinated the Volunteer Lakes Monitoring Program (VLMP) from 1992-2010. The VLMP trained, equipped and supported local volunteers who collected data and reported on over three dozen lakes in the Flathead Basin.

The Environmental Protection Agency (EPA) and FBC programs were the baseline models for the Whitefish to Eureka Volunteer Lake Monitoring Program (VLMP) which was initiated in 2007 by the WLI in partnership with Montana Fish, Wildlife & Parks (MFWP). The Program was established to provide local residents an opportunity to collect baseline data that to help determine the trophic status of lakes and implement early Aquatic Invasive Species (AIS) detection and prevention in Northwest Montana. In 2010, the Whitefish to Eureka VLMP combined with the FBC VLMP to form the NWMTLVMN. The NWMTLVMN currently has more than fifty-five volunteers that monitor a total of fifty locations on forty-one lakes in Flathead, Lake, Lincoln and Missoula counties. The lakes in the Program represent diversity in public use, accessibility and morphology.

Through this program, WLI trains "citizen scientists" to monitor 40 lakes in Flathead, Lincoln, Lake, and Missoula Counties by collecting basic limnological measurements such as water chemistries, hydrolab profiles, and plankton tows that will establish lake trend data over time, and to monitor for the presence of AIS. Many of these lakes previously had no scientific data. The partnership enables WLI to extend its monitoring reach through volunteer efforts, while involving community members in understanding and protecting their natural resources. The NWMTLVMN website www.nwmtlvmn.org allows volunteers to access information, report their data, and stay abreast of AIS issues. Volunteers contribute nearly 1000 hours to NWMTLVMN annually.

Link to report


                  Media Release | Fact Sheet | Full Report

What are Aquatic Invasive Species?
Aquatic invasive species (AIS) are non-native plants and animals that impact water bodies and wetlands. They are species for which a local ecosystem’s native species have no defense mechanisms or for which they cannot compete against for food and shelter. They may start as a nuisance, but can have disastrous long-term effects. AIS can be transported on any type of watercraft, trailers, and angler’s bait buckets or equipment. Some AIS can find their way into interior compartments and watercraft ballasts, and others can “hitchhike” from one water body to another by attaching themselves to surfaces. All AIS are of concern for Montana waterways, but with zebra mussels now in Montana, they pose the greatest current threat.
Once established, AIS can destroy waterways. Invasive mussels, for instance, reproduce so rapidly that their sharp shells blanket shorelines so that footwear must be worn to walk the area. They attach themselves to water circulation systems on watercraft, overheating and destroying motors. Decaying mussels also release an unpleasant odor that permeates the air and water. They reproduce rapidly adhering to any stable surface. If established on water intake pipes, they can cause system failures and expensive clean-ups. How bad are they? In the United States, zebra mussels have cost the power industry over $3 billion between1993–1999, impacting industries, businesses, and communities for over $5 billion. Although mussels tend to dominate the news, additional threats come from a variety of invasive plants, fish, and pathogens. 

History has shown us that zebra mussels quickly clog water intake pipes, impact hydroelectric facilities, and their sharp shells compromise recreational pursuits. Their voluminous filter feeding dramatically alters the food web and overtime degrades water quality. A zebra mussel infestation in Whitefish Lake could result in the City’s drinking water intake pipe in becoming plugged with mussels. The water cooling system in our boat motors could become encrusted with mussels. They could spread across our docks, and our children’s feet could be cut as they wade barefoot into the lake.  Our lake fishery and overall water quality could forever be changed. All of these things would cause indirect consequences to small businesses in Whitefish due to boating and recreation restrictions or closures. And there would be a great loss in property value to homeowners on and near the lake. These are but a few of the numerous consequences of AIS infestations we’ve seen throughout the U.S.

Invasive Mussels in Montana

Until recently, Montana was one of a few remaining western states void of invasive mussels. But in early November 2016, Montana Department of Fish, Wildlife & Parks (MFWP) reported that Tiber Reservoir, east of Shelby, Montana tested positive for zebra mussels. They also reported that Canyon Ferry near Helena had suspect results. Since that time, additional samples from the Milk River downstream of Nelson Reservoir and the Missouri River upstream of Townsend also returned suspect results.

On November 30th, 2016 Governor Bullock issued an executive order declaring a statewide natural resource emergency that included the deployment of an interagency rapid response team to tackle the emerging issue. On December 1st, 2016 the state took further action by issuing emergency orders restricting the launch and removal of boats from Tiber Reservoir and Canyon Ferry. Glacier National Park and the Blackfeet Indian Reservation placed moratorium closures to boating, and the U.S. Fish & Wildlife Service closed Jessup Mill Pond outside of Creston in response to the zebra mussel threat. 2017 ushered in a new paradigm for the public’s interaction with Montana waters. We must all now take an active role in this issue by spreading the word, talking to our elected officials, and supporting local and statewide AIS prevention efforts. 

What is Whitefish Doing to Protect Whitefish Lake?

In 2017, the City of Whitefish, Montana State Parks and the Whitefish Lake Institute (WLI) partnered to bring the robust Our Lake, Our Future: Whitefish Lake Aquatic Invasive Species Management Program to fruition. The goal of this program is to safeguard Whitefish Lake and downstream water resources from the introduction of AIS. The clean and healthy water of Whitefish Lake provides many recreational opportunities such as swimming, boating, and fishing; and serves as a drinking water supply for the City of Whitefish during part of the year. It also imparts extensive economic value to the entire community of and surrounding Whitefish, creating an attractive place to live, work, and recreate. 

History of AIS Programming in Whitefish
Whitefish is perhaps the most progressive community in the state of Montana in addressing AIS issues. Since 2013, WLI has drafted and implemented a Whitefish AIS Management Plan that the Whitefish City Council has approved and funded. Each year, there are various tasks completed for early detection, monitoring and prevention. Some of these tasks include the Whitefish City Beach Watercraft Inspection Station and early detection monitoring of zebra mussels from environmental DNA (eDNA) analysis. Due to the generosity of the Joe and Cindy Gregory Family (WLI Members), an official watercraft inspection station was constructed at City Beach.

One previous gap for Whitefish Lake had been the lack of a watercraft inspection station at State Park. WLI partnered with Montana State Parks and the Montana Department of Natural Resources and Conservation (DNRC) to coordinate and implement a watercraft inspection capability there. Additionally, WLI continues to consult with AIS partners including MFWP, DNRC, University of Montana, and the Conferderated Salish and Kootenai Tribes as we go through the annual planning process. The City of Whitefish Community Services Coordinator, WLI’s Executive Director, and WLI's Science and Education Director also received upper level watercraft inspection and decontamination training. WLI’s annual AIS Management Plan proposal to City Council remains adaptive in addressing the increased threat to our lake and community. In 2017, with funding provided by the Whitefish Community Foundation, WLI purchased a decontamination unit and associated safety equipment.

Since 2011, WLI has also partnered with MFWP to coordinate, administer, and train volunteers for the Northwest Montana Lakes Volunteer Monitoring Network. Through that program, volunteers collect water quality and AIS early detection samples from over 40 lakes in northwest Montana. That early detection sampling includes looking for the microscopic juvenile “veliger” stage of zebra mussels.

Unfortunately, there is no perfect tool or set of tools in our toolbox to totally eliminate the AIS threat to Whitefish Lake. That’s why we need help from the public to clean, drain and dry your watercraft and equipment after each use.

The Beaver Lake Story
Zebra mussels aren’t the only invasive species that can impact Whitefish Lake and our local economy. In October 2011, Eurasian Watermilfoil (EWM) was discovered by the Montana Department of Natural Resources and Conservation near the boat ramp on Beaver Lake near Whitefish.  Beaver Lake is hydrologically connected to Whitefish Lake and there are numerous methods for the plant to be spread from Beaver Lake to Whitefish Lake. An AIS response team—of which WLI was a member—responded to the discovery for further investigation. Bottom barriers were placed over the identified patch and a control/eradication plan was developed by a multiple agency workgroup in which the City of Whitefish and WLI participated. 

If left untreated, EWM forms dense mats of vegetation on the surface of the water that can interfere with recreational activities such as fishing, swimming, and boating, and that threatens the health of the water body. The resulting effect can be the loss of recreational use, decline in ecosystem health, and a decrease in lakefront property values. EWM reproduces successfully and very rapidly and plant fragments can colonize new areas, making it a threat to any water body it invades.

Since 2012, WLI and the City of Whitefish have taken the lead in addressing the EWM issue at Beaver Lake. As part of the Whitefish AIS Management Plan, WLI coordinated a suction dredging operation to eradicate plants. In 2012, 23.5 pounds of EWM was removed. The program has proven successful and in 2017, only 2 plants were removed. This atypical AIS success story is the result of very early detection coupled with rapid and aggressive eradication techniques. Because of the real to Whitefish Lake and the watershed, suction dredging will continue indefinitely until there is confidence that the EWM has been eradicated.

See all the organizations who are partnering on the Aquatic Invasive Species efforts.


Learn more about 

For more photos on Aquatic Invasive Species,
go to the Northwest Montana Lakes Volunteer Monitoring Network website.