A “Peak” into California’s Alpine Lakes and their Food Webs

By Christine A. Parisek

“The Sierra Nevada is five hundred miles of rock put right. Granite freed by glaciers and lifted through clouds where water, frozen and fine, has scraped and washed it into a high country so brilliant it brings light into night.” – Willard Wyman

Alpine lakes are fascinating ecosystems. They are recognized for their clear and pristine appearance, and are mostly cold-water environments nestled into rugged high elevation landscapes. These lakes harbor unique and interesting plant and animal species adapted to thrive in the seemingly harsh environment. The goal of this blog is to introduce California Waterblog readers to California’s alpine lake resources and to highlight the significance of effectively managing these valuable and increasingly vulnerable ecosystems. As a researcher in mountain lake ecology, I’m excited to share some of my field research and provide an overview for why these lakes offer unique opportunities to learn about California’s freshwater resources and food web ecology.


Fig 1. Map of the Cascade-Sierra Province. Source: National Park Service, https://www.nps.gov/articles/cascadesierra.htm.

California’s Sierra Nevada mountain range spans from northern to southern California and is adjacent to the Cascade mountain range. The Sierra is mostly comprised of granite, supplied with volcanic substrate in the north. Lakes in the Sierra are coldwater systems driven by snowmelt and ice dynamics, and >75% of California’s water comes from the Sierra Nevada-Cascade snowpack. In the north where volcanic rock takes over granite, the lakes are able to receive more groundwater inflow. Sierra Nevada lakes >6,000 feet were historically fishless; however, recreational fisheries programs dating back to the mid-1800s made it commonplace to stock fishes in mountain lakes so that now at least 60% of water bodies contain introduced fishes, especially trout. The introduction of a top consumer into these sensitive cold-water systems has negative and well-known ripple effects on the native biota and the entire food web.

Fieldwork in high mountain lakes 

My ongoing research specifically explores lake food web structure and function across heterogeneous mountain landscapes. For the past four summers I’ve led a field crew to remote mountain lakes in the Sierra Nevada to sample lake food webs as part of the “Sierra Fishes” Project. My team each backpacks ~75lbs into the backcountry to sample as many lake food webs as we can over the summers. We carry a cooler filled with dry ice for sample storage, an inflatable packraft, fish nets and various measuring supplies, a van dorn water sampler, plankton net, aquatic insect survey gear, and of course camping gear and food. We do our best to pack light (spoon toothbrush, anyone?) but field gear just weighs what it weighs! (Fun fact: 30lbs of dry ice only lasts about 4 days in the mountains!) Volumetrically, the study lakes range 20,000 – 48,000,000 m3 and are selected to be at a roughly constant elevation within each basin; thus the sampled systems span 3 orders of magnitude in volume. The lakes harbor a range of fishes, including golden trout, brook trout, rainbow trout, brown bullhead catfish, speckled dace, tui chub, suckers, and shiner; though usually no more than 1-3 fish species will be present per lake. Sampling a whole lake food web means we collect bits of tissue from anything living in the lake – fishes, zooplankton, aquatic insects, algae, plants, diatoms – we put the samples on ice and trek them back to the lab for workup and isotope analysis. By analyzing the isotope data of the tissues, we can reconstruct a comprehensive food web that sheds light on dynamics of the lake’s ecology, functioning, and the roles of organisms within each lake. This information is valuable for effective lake management and future conservation efforts.

Fig 2. Emily Jacinto inflates a packraft at a mountain lake in the Sequoia-Kings Canyon National Park. Photo by Christine Parisek.

Cottonwood Lakes 

Fig 3 (Top). Excerpt from the paper: Curtis, B., 1934. The golden trout of Cottonwood Lakes (Salmo agua-bonita Jordan). Transactions of the American Fisheries Society, 64(1), pp.259-265.
Fig 4 (Bottom). Three California golden trout exhibiting different spot patterns. Photo by Christine Parisek.

One of my favorite regions in the Sierra Nevada is the Cottonwood Lakes Basin. Backpackers in this area will often be acclimatizing to high elevation prior to scaling Mt. Whitney (14,505 ft), the tallest peak in the contiguous United States. You’ll likely also run into the organizers of the Golden Trout Wilderness School at Golden Trout Camp, who shared with our crew aspects of the forest most people miss on the famed hike. The Cottonwood Lakes are at high elevation (~11,000 ft), represent a collection of moraine lakes, and are home to several populations of introduced and isolated California golden trout (Oncorhynchus mykiss aguabonita). Golden trout, the California state fish, are native to just two streams in Southern California (Golden Trout Creek and the South Fork Kern River). Golden trout’s arrival into the Cottonwood Lakes was, as Curtis (1934) describes, “in 1876… thirteen fish were carried by ranchers in a tea-pot across the divide into Cottonwood Creek… in 1891 a further transplant was made… to the lakes…”. Currently, golden trout are maintained at the lakes and managed by the California Department of Fish and Wildlife as a source of eggs for the Mt. Whitney Hatchery. … And, they are notoriously difficult to catch on a fly! (Fig. 5: a cold Mackenzie in the wilderness, without a fish, shrugging).

Fig 5. A cold Mackenzie Miner in the wilderness, without a fish, shrugging. Photo by Colby Hause.

Managing mountain lakes

Mountain lakes in California span the entire state, they hold vulnerable and endemic species, and contribute substantially to recreational fisheries, yet they do not receive the same attention or funding as other local systems. 

Understanding mechanisms that drive lake ecosystems in the mountains is a tricky business. You might think all mountain lakes are the same, so why bother trying to reach so many? Well, they are not! Large vs small lakes, high elevation vs lower montane lakes, and even northern California vs southern California lakes are just a few contributing factors that can truly drive the ecology and ecosystem dynamics of waterbodies. The lakes are highly sensitive to climate change, snowmelt dynamics, and wildfire activity, and are therefore indicators of the health of the surrounding landscape overall.

At the regional scale, we face many questions such as – What is happening to these fragile systems over time? How will the ecology of lakes respond to climate change? How can we better understand lake stressors and habitat fragmentation or loss? What role does wildfire play in this dynamic? Which lakes should be managed for fisheries, and which not?

Owing to the difficulty in accessing these sites, the numerous waterbodies, and the short lake ice-off window providing the opportunity to do so (approximately June – September), high elevation aquatic habitats are generally just poorly studied systems. The Sierra Nevada, with >12K waterbodies, is no exception. Conducing any fieldwork also encompasses major tradeoff – you must choose to either cover a lot of ground with a light sampling regime or perform extensive sampling but ultimately reach fewer total locations. Ultimately these two styles will address different types of research questions. 

Alpine lakes in California are a beautiful and underappreciated natural resource. One of the goals of my work is to raise awareness about the importance of lakes to the ecology of California more broadly. Additionally, lakes can be useful for testing ecological principles of broader relevance (Carpenter et al. 1985; Scheffer et al. 2001; Shurin et al. 2002; Carpenter et al. 2011). I hope to provide more blogs on my work with these lakes in the future!

Christine Parisek is a Ph.D. candidate in the Graduate Group in Ecology at UC Davis and a science communications fellow at the Center for Watershed Sciences.

Fig 6. A stormy afternoon in the Tahoe National Forest. Photo by Christine Parisek.

Further Reading

Carpenter, S.R., Cole, J.J., Pace, M.L., Batt, R., Brock, W.A., Cline, T., Coloso, J., Hodgson, J.R., Kitchell, J.F., Seekell, D.A. and Smith, L., Weidel B. 2011. Early warnings of regime shifts: a whole-ecosystem experiment. Science, 332(6033), pp.1079-1082.

Carpenter, S.R., Kitchell, J.F. and Hodgson, J.R., 1985. Cascading trophic interactions and lake productivity. BioScience, 35(10), pp.634-639.

Curtis, B., 1934. The golden trout of Cottonwood Lakes (Salmo agua-bonita Jordan). Transactions of the American Fisheries Society, 64(1), pp.259-265.

Eby, L.A., Roach, W.J., Crowder, L.B. and Stanford, J.A., 2006. Effects of stocking-up freshwater food webs. Trends in ecology & evolution, 21(10), pp.576-584.

Knapp, R.A., 1996. Non-native trout in natural lakes of the Sierra Nevada: an analysis of their distribution and impacts on native aquatic biota. In Sierra Nevada ecosystem project: final report to Congress (Vol. 3, pp. 363-407). University of California, Davis: Centers for Water and Wildland Resources.

Kraemer, B.M., Pilla, R.M., Woolway, R.I., Anneville, O., Ban, S., Colom-Montero, W., Devlin, S.P., Dokulil, M.T., Gaiser, E.E., Hambright, K.D. and Hessen, D.O., Higgins S.N., Jöhnk K.D., Keller W., Knoll L.B., Leavitt P.R., Lepori F., Luger M.S., Maberly S.C., Müller-Navarra D.C., Paterson A.M., Pierson D.C., Richardson D.C., Rogora M., Rusak J.A., Sadro S., Salmaso N., Schmid M., Silow E.A., Sommaruga R., Stelzer J.A.A., Straile D., Thiery W., Timofeyev M.A., Verburg P., Weyhenmeyer, G.A., Adrian, R. 2021. Climate change drives widespread shifts in lake thermal habitat. Nature Climate Change, 11(6), pp.521-529.

Moser, K.A., Baron, J.S., Brahney, J., Oleksy, I.A., Saros, J.E., Hundey, E.J., Sadro, S., Kopáček, J., Sommaruga, R., Kainz, M.J. and Strecker, A.L., Chandra S., Walters D.M., Preston D.L., Michelutti N., Lepori F., Spaulding S.A., Christianson K.R., Melack J.M., Smol J.P. 2019. Mountain lakes: Eyes on global environmental change. Global and Planetary Change, 178, pp.77-95.

Parisek, C.A., Marchetti, M.P. and Cover, M.R., 2023. Morphological plasticity in a caddisfly that co-occurs in lakes and streams. Freshwater Science, 42(2), pp.161-175. 

Scheffer, M., Carpenter, S., Foley, J.A., Folke, C. and Walker, B., 2001. Catastrophic shifts in ecosystems. Nature, 413(6856), pp.591-596.

Schmeller, D.S., Urbach, D., Bates, K., Catalan, J., Cogălniceanu, D., Fisher, M.C., Friesen, J., Füreder, L., Gaube, V., Haver, M. and Jacobsen, D., Roux G.L., Lin Y., Loyau A., Machate O., Mayer A., Palomo I., Plutzar C., Sentenac H., Sommaruga R., Tiberti R., Ripple W.J. 2022. Scientists’ warning of threats to mountains. Science of the Total Environment, 853, p.158611.

Shurin, J.B., Borer, E.T., Seabloom, E.W., Anderson, K., Blanchette, C.A., Broitman, B., Cooper, S.D. and Halpern, B.S., 2002. A cross‐ecosystem comparison of the strength of trophic cascades. Ecology Letters, 5(6), pp.785-791.

Smits, A.P., MacIntyre, S. and Sadro, S., 2020. Snowpack determines relative importance of climate factors driving summer lake warming. Limnology and Oceanography Letters, 5(3), pp.271-279.

General Interest

Video: How fish are stocked in high elevation lakes, Youtube, https://www.youtube.com/watch?v=-nwNISOQLsw

Video: Zooplankton sampling in an alpine lake for the “Sierra Fishes” Project, Christine Parisek,  https://twitter.com/caparisek/status/1546210839287345152?s=20

Video: “Stream Macroinvertebrates, A Love Story” by Kyle Phillips, Center for Watershed Sciences Youtube Channel, https://www.youtube.com/watch?v=ReCOnps2jeI

Natural History of the Sierra Nevada, California Naturalist Series 2015, https://anrcatalog.ucanr.edu/pdf/8535.pdf

Water Supply in the Sierra Nevada, Sierra Nevada Conservancy, https://sierranevada.ca.gov/what-we-do/water-supply/

Cottonwood Lakes Trail, Forest Service, https://www.fs.usda.gov/recarea/inyo/recarea/?recid=2089

Scaling Mt. Whitney, recreation.gov, https://www.recreation.gov/permits/445860

Golden Trout Wilderness School Summer Programs, http://www.goldentroutwildernessschool.org/

California Golden Trout, California Department of Fish and Wildlife, https://wildlife.ca.gov/Conservation/Fishes/California-Golden-Trout

California Golden Trout, California Trout, https://caltrout.org/sos/species-accounts/trout/california-golden-trout

NSF RAPID: Food webs of 10 lakes before and after a mega-wildfire, https://watershed.ucdavis.edu/news/2022/06/25/nsf-rapid-food-webs-10-lakes-after-mega-wildfire

SOS II: Fish in Hot Water, California Trout, https://caltrout.org/sos

About Andrew Rypel

Andrew L. Rypel is a Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and Director of the Center for Watershed Sciences.
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2 Responses to A “Peak” into California’s Alpine Lakes and their Food Webs

  1. Bruce McCrea says:

    I love Christine’s style she adds readability to science! (more often missed) Having enjoyed Desolation Valley, Minarretts(sp) Wilderness, & John Muir Wilderness 65 years ago I applaud her effort(and yours) to preserve my memories.(stepping over the San Joaquin river & being surrounded by 7 ten thousand foot mountains)

  2. Ted Swift says:

    Doctor-to-be Parisek gets the balance of conveying complex science accessibly; great article! I’m tickled to see this kind of sophisticated study moving into the higher elevations. A couple of decades ago while studying limnology at UCD, I thought about ways of using, say, a backpackable radio-controlled solar-recharged boat (we’d call it a drone now) to make physical and chemical measurements in lakes. But thoughts are cheap: Christine and her team are actually doing it, studying the biology and ecology, which is a lot harder than mere physical measurements.

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