What Happens to Cyanobacteria and Algae in Winter—and Why Sediment Still Matters
A winter ecology primer for lake and pond programs (with practical management takeaways)
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In ice-covered lakes, biology slows—but it rarely stops. Winter is the lake’s pre-season: ice and snow control light, oxygen tends to drop, and sediments store nutrients and “seed banks” (resting cells) that restart populations in spring. Those starting conditions shape how quickly the lake ramps up after ice-out—and how easily cyanobacteria can take over in summer (Jakobsson, 2025; Wilhelm et al., 2024).
Winter sets the stage for spring and summer
Ice puts a lid on the lake. Wind can’t mix the water, and snow/ice act like sunglasses. That controls under-ice growth, oxygen drawdown, and how easily bottom nutrients get stirred up. At ice-out, those settings carry into spring—and can tilt summer bloom risk (Jakobsson, 2025; Wilhelm et al., 2024).
Where do cyanobacteria and algae go?
Some algae and cyanobacteria hang on in the water column at low gear. Cold-loving groups—especially diatoms—can still grow under ice when light is decent, helping kick-start the spring food web (Jakobsson, 2025; Wilhelm et al., 2024).
Other bloom-formers head for the mud. Many cyanobacteria make akinetes—thick-walled survival cells that sink and wait, then “wake up” when conditions improve. These time-capsules can reseed the water column months later (Ho et al., 2024).
Figure 1. Akinete of Dolichospermum smithii. Photo: Panek (CC BY-SA 3.0 PL). (Panek, 2012).
Can cyanobacteria bloom under ice?
Yes—just less often than in midsummer. Under-ice cyanobacteria blooms have been reported in temperate and boreal lakes, often during clear-ice winters (more light) or after mixing events that move nutrients around (Wejnerowski et al., 2018; Rybak et al., 2024; Grosbois et al., 2024).
Winter blooms are usually smaller and easier to miss, but they can still shift spring timing—and some taxa can retain toxin-producing potential even in cold conditions (Rybak et al., 2024; Grosbois et al., 2024).
Winter biogeochemistry: oxygen decline and internal loading
With ice on top, the lake can’t “breathe” with the atmosphere. Oxygen isn’t replenished as easily, while respiration and decomposition keep chewing through it—especially in shallow, nutrient-rich, or high-organic systems (Davis et al., 2020; Zdorovennova et al., 2021).
As bottom waters lose oxygen, sediment chemistry shifts and nutrients can recycle more readily. This can contribute to “internal loading”—phosphorus released from sediments—which can jump-start early-season growth even when external inputs are controlled (Zdorovennova et al., 2021; James, 2016).
Figure 2. Cyanobacteria bloom beneath ice (Vienna City Lake, Illinois; Jan 6, 2021). Source: Illinois EPA. (Illinois EPA, 2021).
The winter microbial engine: biology that carries into summer
Winter under ice is less a pause and more a re-balance. With less light for algae, bacteria do more of the cleanup—breaking down dissolved organic matter and recycling nutrients while respiration keeps humming (Jakobsson, 2025; Wilhelm et al., 2024; Zdorovennova et al., 2021).
Three winter moves can echo into spring and summer:
- Mixotrophy (best of both worlds): some algae can photosynthesize and snack on bacteria—handy when sunlight is scarce but prey is available (Jakobsson, 2025; Wilhelm et al., 2024).
- Seed banks (the lake’s savings account): akinetes and other resting stages sit in sediments and repopulate fast once light and temperature climb (Ho et al., 2024).
- Light-driven timing: clearer ice and less snow can boost under-ice growth and change who gets the early-spring head start, with ripple effects on summer bloom risk (Jakobsson, 2025; Wilhelm et al., 2024; Grosbois et al., 2024)
What this means for managers
Summer monitoring is still key, but winter is the setup: it influences who survives and whether oxygen is drawn down. When oxygen runs low and sediments recycle nutrients, spring can start on a cyanobacteria-friendly footing (Wejnerowski et al., 2018; Davis et al., 2020; Zdorovennova et al., 2021; James, 2016).
Where Polar Blend and MuckBiotics Zero fit
Winter leverage often comes from tackling the background drivers—organic matter and sediment conditions—rather than chasing visible blooms. Polar Blend is designed for cold water to support microbial activity under ice so decomposition doesn’t fully stall for months (Natural Lake Biosciences, n.d.-a).
MuckBiotics Zero plays the longer game: reducing organic muck can lower oxygen demand and ease nutrient recycling pressure over time, without adding nutrient inputs that could act like fertilizer for algae (Natural Lake Biosciences, n.d.-b).
Used together, the goal isn’t to force “summer biology” in January. It’s to lower the spring starting line: less reactive organic matter, less oxygen drawdown, and less nutrient push from the bottom as waters warm—making summer blooms less likely.
References
Davis, M.N., McMahon, T.E., Cutting, K.A., et al. 2020. Environmental and climatic factors affecting winter hypoxia in a freshwater lake: evidence for a hypoxia refuge and for re-oxygenation prior to spring ice loss. Hydrobiologia. https://doi.org/10.1007/s10750-020-04382-z
Grosbois, G., Anjum Mou, T., & Montoro Girona, M. 2024. Cyanobacteria in winter: Seasonal dynamics of harmful algal blooms and their driving factors in boreal lakes. Heliyon. https://www.sciencedirect.com/science/article/pii/S2405844024167187
Ho, H.-I., Park, C.-H., Yoo, K.-E., Kim, N.-Y., & Hwang, S.-J. 2024. Survival and Development Strategies of Cyanobacteria through Akinete Formation and Germination in the Life Cycle. Water 16(5):770. https://doi.org/10.3390/w16050770
Illinois Environmental Protection Agency. 2021. Cyanobacteria bloom beneath ice (Vienna City Lake, Jan 6, 2021) [photograph]. https://epa.illinois.gov/content/dam/soi/en/web/epa/topics/water-quality/monitoring/algal-bloom/publishingimages/pages/identifying/vienna-cc-lake-1-6-21.jpg
Illinois Environmental Protection Agency. n.d. Identifying Cyanobacteria Blooms. https://epa.illinois.gov/topics/water-quality/monitoring/algal-bloom/identifying.html
Jakobsson, E. 2025. Lake food webs under changing winter conditions. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2613. Acta Universitatis Upsaliensis. https://uu.diva-portal.org/smash/get/diva2:2013965/FULLTEXT01.pdf
James, W. 2016. Internal P Loading: A Persistent Management Problem in Lake Recovery. Lakeline (Spring 2016), North American Lake Management Society. https://www.nalms.org/wp-content/uploads/2017/01/36-1-3.pdf
Natural Lake Biosciences. n.d.-a. Polar Blend. https://naturallake.com/product/polar-blend/
Natural Lake Biosciences. n.d.-b. MuckBiotics Zero. https://naturallake.com/product/muckbiotics-zero
Panek. 2012. Dolichospermum smithii – akinete (photomicrograph). Wikimedia Commons. https://commons.wikimedia.org/wiki/File:Dolichospermum_smithii_-_akinete.jpg
Rybak, M., Rosińska, J., Wejnerowski, Ł., Rodrigo, M.A., & Joniak, T. 2024. Community Structure and Toxicity Potential of Cyanobacteria during Summer and Winter in a Temperate-Zone Lake Susceptible to Phytoplankton Blooms. Toxins 16(8):357. https://www.mdpi.com/2072-6651/16/8/357
Wang, C., Zhang, Y., Li, H., & Morrison, R.J. 2013. Sequential extraction procedures for the determination of phosphorus forms in sediment. Limnology 14:147–157. https://doi.org/10.1007/s10201-012-0397-1
Wejnerowski, Ł., Rzymski, P., Kokociński, M., & Meriluoto, J. 2018. The structure and toxicity of winter cyanobacterial bloom in a eutrophic lake of the temperate zone. Ecotoxicology 27:752–760. https://doi.org/10.1007/s10646-018-1957-x
Wilhelm, S., Zepernick, B., & McKay, R.M. 2024. Losing winter ice is changing the Great Lakes food web – here’s how light is shaping life underwater. The Conversation (republished by University of Tennessee Knoxville). https://news.utk.edu/2024/06/13/the-conversation-losing-winter-ice-is-changing-the-great-lakes-food-web-heres-how-light-is-shaping-life-underwater
Zdorovennova, G., Palshin, N., Golosov, S., et al. 2021. Dissolved Oxygen in a Shallow Ice-Covered Lake in Winter: Effect of Changes in Light, Thermal and Ice Regimes. Water 13(17):2435. https://www.mdpi.com/2073-4441/13/17/2435
Tip of the day:
Cyanobacteria can form resting cells (akinetes) that overwinter in sediment and help restart blooms in spring. Winter muck-focused management—Polar Blend and MuckBiotics Zero—can reduce that stored fuel before summer.
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MuckBiotics Zero
About the Author
Landon earned a Bachelor of Science degree from the University of Wisconsin – Madison. He joined the Aquafix team in 2011 and currently leads the Natural Lake Biosciences division. Landon serves on the Board of Directors for the Midwest Aquatic Plant Management Society and is a contributing member of many professional aquatic organizations. He is passionate about using his industry experience and expertise to promote sustainable and effective biological technologies for managing aquatic resources.
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