Editing Great Lakes (section)

==Ecology==
{{stack|[[File:USGS image cropped.jpg|thumb|upright=1.5|Generalized schematic of Great Lakes waterline ecosystem]]}}

Historically, the Great Lakes, in addition to their [[lake ecology]], were surrounded by various [[forest]] ecoregions (except in a relatively small area of southeast Lake Michigan where [[savanna]] or [[prairie]] occasionally intruded). Logging, urbanization, and agriculture uses have changed that relationship. In the early 21st century, Lake Superior's shores are 91% forested, Lake Huron 68%, Lake Ontario 49%, Lake Michigan 41%, and Lake Erie, where logging and urbanization has been most extensive, 21%. Some of these forests are second or third growth (i.e. they have been logged before, changing their composition). At least 13 wildlife species are documented as becoming extinct since the arrival of Europeans, and many more are threatened or endangered.<ref name=Grady/> Meanwhile, exotic and invasive species have also been introduced.

===Fauna===
{{see also|Great Lakes Areas of Concern#Invasive species|Category:Fauna of the Great Lakes region (North America)|Category:Fish of the Great Lakes|Asian carp in North America}}
[[File:Lakesturgeon public U.S.Fish&Wildlife.jpg|thumb|[[Lake sturgeon]], the largest native fish in the Great Lakes and the subject of extensive commercial fishing in the 19th and 20th centuries is listed as a threatened species<ref>{{cite web |url = http://www.fws.gov/midwest/sturgeon/biology.htm |title = Great Lakes Lake Sturgeon Web Site |author = U.S. Fish and Wildlife Service }}</ref>]]
While the organisms living on the bottom of shallow waters are similar to those found in smaller lakes, the deep waters contain organisms found only in deep, cold lakes of the northern latitudes. These include the delicate opossum shrimp (order [[mysida]]), the deepwater scud (a crustacean of the order [[amphipoda]]), two types of [[copepod]]s, and the [[deepwater sculpin]] (a spiny, large-headed fish).<ref>{{cite web |url = https://www.britannica.com/place/Great-Lakes |title = Great Lakes |last1 = Beeton |first1 = Alfred |website = Encyclopædia Britannica |access-date = January 31, 2016 }}</ref>

The Great Lakes are an important source of [[fishing]]. Early European settlers were astounded by both the variety and quantity of fish; there were 150 different species in the Great Lakes.<ref name="Grady" /> Throughout history, fish populations were the early indicator of the condition of the Lakes and have remained one of the key indicators even in the current era of sophisticated analyses and measuring instruments. According to the bi-national (U.S. and Canadian) resource book, ''The Great Lakes: An Environmental Atlas and Resource Book'': "The largest Great Lakes fish harvests were recorded in 1889 and 1899 at some {{convert|67000|t|ton}} [147&nbsp;million pounds]."<ref name="glearb">{{cite book |author = Anon |year = 1972 |title = The Great Lakes: An Environmental Atlas and Resource Book }} Bi-national (U.S. and Canadian) resource book.{{full citation needed|date=March 2024}}</ref>

By 1801, the [[New York State Legislature|New York Legislature]] found it necessary to pass regulations curtailing obstructions to the natural migrations of [[Atlantic salmon]] from Lake Erie into their spawning channels. In the early 19th century, the government of [[Upper Canada]] found it necessary to introduce similar legislation prohibiting the use of weirs and nets at the mouths of Lake Ontario's tributaries. Other protective legislation was passed, but enforcement remained difficult.<ref name="Bogue2001m">{{cite book |first = Margaret Beattie |last = Bogue |title = Fishing the Great Lakes: An Environmental History, 1783–1933 |url = https://books.google.com/books?id=Pn7IlRl8DhsC&pg=PA180 |year = 2001 |publisher = Univ of Wisconsin Press |isbn = 978-0-299-16763-9 |page = 180 }}</ref>

On both sides of the Canada–United States border, the proliferation of [[dam]]s and impoundments have multiplied, necessitating more regulatory efforts. Concerns by the mid-19th century included obstructions in the rivers which prevented salmon and [[lake sturgeon]] from reaching their spawning grounds. The Wisconsin Fisheries Commission noted a reduction of roughly 25% in general fish harvests by 1875. The states have removed dams from rivers where necessary.{{Clarify|date=September 2012}}<ref name="Commission">{{cite book |author = Atlantic States Marine Fisheries Commission |title = Special report&nbsp;... of the Atlantic States Marine Fisheries Commission |publisher = The Commission |page = 23 }}</ref>

Overfishing has been cited as a possible reason for a decrease in population of various [[freshwater whitefish|whitefish]], important because of their culinary desirability and, hence, economic consequence. Moreover, between 1879 and 1899, reported whitefish harvests declined from some 24.3&nbsp;million pounds (11&nbsp;million&nbsp;kg) to just over 9&nbsp;million pounds (4&nbsp;million&nbsp;kg).<ref name="MacdonaldService2009"/> By 1900, commercial fishermen on Lake Michigan were hauling in an average of 41&nbsp;million pounds of fish annually.<ref name=js2/> By 1938, Wisconsin's commercial fishing operations were motorized and mechanized, generating jobs for more than 2,000 workers, and hauling 14&nbsp;million pounds per year.<ref name=js2/> The population of giant freshwater mussels was eliminated as the mussels were harvested for use as buttons by early Great Lakes entrepreneurs.<ref name="MacdonaldService2009">{{cite book |editor1-last = Macdonald |editor1-first = David |editor2-last = Service |editor2-first = Katrina |title = Key Topics in Conservation Biology |url = https://books.google.com/books?id=flEwoquwpGUC&pg=PA188 |year = 2009 |publisher = John Wiley & Sons |isbn = 978-1-4443-0906-5 |page = 188 }}</ref>

''The Great Lakes: An Environmental Atlas and Resource Book'' (1972) notes: "Only pockets remain of the once large commercial fishery."<ref name="glearb" /> Water quality improvements realized during the 1970s and 1980s, combined with successful salmonid stocking programs, have enabled the growth of a large recreational fishery.<ref name="Agency1998">{{cite book |title = Great Minds?, Great Lakes! Don't Miss The Boat With Environmental Education |date = March 1997 |url = https://books.google.com/books?id=SlD57QnxOb0C&pg=PA7 |publisher = Environmental Protection Agency |page = 7 }}</ref> The last commercial fisherman left Milwaukee in 2011 because of overfishing and anthropogenic changes to the [[biosphere]].<ref name="js2">{{cite news |url = http://www.jsonline.com/news/wisconsin/127610953.html |title = The lake left me. It's gone |work = Milwaukee Journal Sentinel |date = August 13, 2011 }}</ref>
[[File:Lake Superior North Shore(v2).jpg|thumb|Cliffs at [[Palisade Head]] on Lake Superior in Minnesota near Silver Bay.]]

=== Invasive species ===
Since the 19th century, an estimated 160 new species have found their way into the Great Lakes ecosystem; many have become invasive; the overseas ship ballast and ship hull parasitism are causing severe economic and ecological impacts.<ref>{{cite news |title=New EPA rules to target invasive species; Invaders have plagued Great Lakes for years |newspaper=The Blade|id = {{ProQuest|380761083}}}}</ref><ref name="ISEA">{{cite web |url = http://www.greatlakeseducation.org/about_isea/?id=204 |archive-url = https://web.archive.org/web/20130403134459/http://www.greatlakeseducation.org/about_isea/?id=204 |archive-date = April 3, 2013 |title = Our Threatened Great Lakes |access-date = November 30, 2007 |publisher = Inland Seas Education Association }}</ref> According to the Inland Seas Education Association, on average a new species enters the Great Lakes every eight months.<ref name="ISEA" /> Introductions into the Great Lakes include the [[zebra mussel]], which was first discovered in 1988, and [[quagga mussel]] in 1989. Since 2000, the invasive quagga mussel has smothered the bottom of Lake Michigan almost from shore to shore, and their numbers are estimated at 900&nbsp;trillion.<ref name="js2"/> The [[Mollusca|mollusks]] are efficient filter feeders, competing with native mussels and reducing available food and spawning grounds for fish. In addition, the mussels may be a nuisance to industries by clogging pipes. The [[U.S. Fish and Wildlife Service]] estimated in 2007 that the economic impact of the zebra mussel could be about $5&nbsp;billion over the next decade.<ref>{{cite web |url = http://www.glc.org/ans/ |title = Great Lakes Aquatic Nuisance Species |access-date = November 30, 2007 |publisher = Great Lakes Commission |date = March 27, 2007 |url-status = deviated |archive-url = https://web.archive.org/web/20070415222144/http://www.glc.org/ans/ |archive-date = April 15, 2007 }}</ref>{{Update inline|date=September 2021}} The state of Michigan has had to develop legislation and regulations to help protect against these invasive species. [[Aquatic invasive species regulations in Michigan]] have been put in place to combat the influx of species.

[[File:Zebra mussel GLERL 3.jpg|thumb|upright|A zebra mussel–encrusted vector-averaging [[current meter]] from Lake Michigan.]]

The [[alewife (fish)|alewife]] first entered the system west of Lake Ontario via 19th-century canals. By the 1960s, the small silver fish had become a familiar nuisance to beach goers across Lakes Michigan, Huron, and Erie. Periodic mass die-offs result in vast numbers of the fish washing up on shore; estimates by various governments have placed the percentage of Lake Michigan's biomass which was made up of alewives in the early 1960s as high as 90%. In the late 1960s, the various state and federal governments began stocking several species of salmonids, including the native lake trout as well as non-native [[Chinook salmon|chinook]] and [[Coho salmon|coho]] salmon; by the 1980s, alewife populations had dropped drastically.<ref>{{cite web |last = Smith |first = Paul |title = Gobies up, alewives down in Lake Michigan |url = http://www.jsonline.com/blogs/sports/40240287.html |publisher = Miwaukee Journal Sentinel |access-date = August 6, 2010 |date = February 24, 2009 |url-status = dead |archive-url = https://web.archive.org/web/20110605165415/http://www.jsonline.com/blogs/sports/40240287.html |archive-date = June 5, 2011 }}</ref> The [[ruffe]], a small [[percid]] fish from Eurasia, became the most abundant fish species in Lake Superior's [[Saint Louis River (Lake Superior tributary)|Saint Louis River]] within five years of its detection in 1986. Its range, which has expanded to Lake Huron, poses a significant threat to the lower lake fishery.<ref>{{cite web |title = Predicting Invasive Species in the Great Lakes |url = http://www.epa.gov/ord/sciencenews/scinews_great_lakes.htm |publisher = Environmental Protection Agency |archive-url = https://web.archive.org/web/20110205183050/http://www.epa.gov/ord/sciencenews/scinews_great_lakes.htm |archive-date = February 5, 2011 |url-status = dead }}</ref> Five years after first being observed in the St. Clair River, the [[round goby]] can now be found in all of the Great Lakes. The goby is considered undesirable for several reasons: it preys upon bottom-feeding fish, overruns optimal habitat, spawns multiple times a season, and can survive poor water quality conditions.<ref>{{cite web |last = Glassner-Shwayder |first = Katherine |title = Briefing Paper: Great Lakes Nonindigenous Invasive Species |url = http://www.glc.org/ans/pdf/briefpapercomplete.pdf |archive-url = https://web.archive.org/web/20051227060749/http://www.glc.org/ans/pdf/briefpapercomplete.pdf |archive-date = December 27, 2005 |publisher = Great Lakes Nonindigenous Invasive Species Workshop |access-date = August 6, 2010 |date = July 2000 }}</ref>

The influx of parasitic [[lamprey]] populations after the development of the Erie Canal and the much later Welland Canal led to the two federal governments of the United States and Canada working on joint proposals to control it. By the mid-1950s, the [[lake trout]] populations of Lakes Michigan and Huron were reduced, with the lamprey deemed largely to blame. This led to the launch of the bi-national [[Great Lakes Fishery Commission]].

Several species of exotic [[Cladocera|water fleas]] have accidentally been introduced into the Great Lakes, such as the spiny waterflea, ''[[Bythotrephes longimanus]]'', and the fishhook waterflea, ''[[Cercopagis pengoi]]'', potentially having an effect on the [[zooplankton]] population. Several species of [[crayfish]] have also been introduced that may contend with native crayfish populations. More recently an electric fence has been set up across the Chicago Sanitary and Ship Canal in order to keep several species of invasive [[Asian carp]] out of the lakes. These fast-growing planktivorous fish have heavily colonized the Mississippi and Illinois river systems.<ref>{{cite web |title = Risk Assessment for Asian Carps in Canada |url = http://www.dfo-mpo.gc.ca/csas/Csas/DocREC/2004/RES2004_103_E.pdf |archive-url = https://web.archive.org/web/20060301092522/http://www.dfo-mpo.gc.ca/csas/Csas/DocREC/2004/RES2004_103_E.pdf |archive-date = March 1, 2006 |url-status = live |publisher = CSAS |date = 2004 }}</ref> Invasive species, particularly zebra and quagga mussels, may be at least partially responsible for the collapse of the deepwater demersal fish community in Lake Huron,<ref>{{cite journal |last1 = Riley |first1 = S.C. |year = 2008 |title = Deepwater demersal fish community collapse in Lake Huron |journal = Transactions of the American Fisheries Society |volume = 137 |issue = 6 |pages = 1879–90 |url = http://www.glsc.usgs.gov/_files/publications/1457.pdf |archive-url = https://web.archive.org/web/20130603123219/http://www.glsc.usgs.gov/_files/publications/1457.pdf |archive-date = June 3, 2013 |doi = 10.1577/T07-141.1 |last2 = Roseman |first2 = Edward F. |last3 = Nichols |first3 = S. Jerrine |last4 = O'Brien |first4 = Timothy P. |last5 = Kiley |first5 = Courtney S. |last6 = Schaeffer |first6 = Jeffrey S. |bibcode = 2008TrAFS.137.1879R }}</ref> as well as drastic unprecedented changes in the zooplankton community of the lake.<ref>{{cite journal |year = 2009 |title = Recent shifts in the crustacean zooplankton community of Lake Huron |doi = 10.1139/F09-036 |journal = Canadian Journal of Fisheries and Aquatic Sciences |volume = 66 |pages = 816–828 |last1 = Barbiero |first1 = Richard P. |last2 = Balcer |first2 = Mary |last3 = Rockwell |first3 = David C. |last4 = Tuchman |first4 = Marc L. |issue = 5 }}</ref>

===Microbiology===
Scientists understand that the micro-aquatic life of the lakes is abundant but know very little about some of the most plentiful microbes and their environmental effects in the Great Lakes. Although a drop of lake water may contain 1&nbsp;million [[bacteria]] cells and 10&nbsp;million [[viruses]], only since 2012 has there been a long-term study of the lakes' micro-organisms. Between 2012 and 2019 more than 160 new species have been discovered.<ref>{{cite news |url = https://www.chicagotribune.com/news/environment/ct-lake-michigan-microbes-20190705-ihsj56fbs5d4ngvyljsjsg5ao4-story.html |title = Minuscule microbes wield enormous power over the Great Lakes. But many species remain a mystery. |last = Briscoe |first = Tony |date = July 5, 2019 |work = Chicago Tribune |access-date = July 5, 2019 }}</ref>

===Flora===
{{category see also|Flora of the Great Lakes region (North America)}}
Native habitats and ecoregions in the Great Lakes region include:

* [[Alvar]]
* [[Fen#Rich fens|Boreal rich fen]] (such as in [[Flora of Door County, Wisconsin#Plant communities unique to the area|Door County]])
* [[Eastern forest-boreal transition]]
* [[Eastern Great Lakes lowland forests]]
* [[Southern Great Lakes forests]]
* [[Central forest-grasslands transition]]
* [[Upper Midwest forest-savanna transition]]
* [[Western Great Lakes forests]]
* [[Central Canadian Shield forests]]
* [[Laurentian Mixed Forest Province]]
* [[Beech-maple forest]]
* [[Habitats of the Indiana Dunes]]

Plant lists include:
* [[List of Michigan flowers]]
* [[List of Minnesota wild flowers]]
* [[List of Minnesota trees]]

==== Logging ====

[[Logging]] of the extensive forests in the Great Lakes region removed [[riparian zone|riparian]] and adjacent tree cover over rivers and streams, which provide shade, moderating water temperatures in fish spawning grounds. Removal of trees also destabilized the soil, with greater volumes washed into stream beds causing siltation of gravel beds, and more frequent flooding.

Running cut logs down the tributary rivers into the Great Lakes also dislocated sediments. In 1884, the New York Fish Commission determined that the dumping of sawmill waste (chips and sawdust) had impacted fish populations.<ref name="Dempsey2004">{{cite book |last = Dempsey |first = Dave |title = On the Brink: The Great Lakes in the 21st Century |year = 2004 |publisher = Michigan State University Press |isbn = 978-0-87013-705-1 |page = [https://archive.org/details/onbrinkgreatlake0000demp/page/48 48] |url-access = registration |url = https://archive.org/details/onbrinkgreatlake0000demp/page/48 }}</ref>

===Pollution===
The first U.S. [[Clean Water Act]], passed by a Congressional override after being vetoed by U.S. President [[Richard Nixon]] in 1972, was a key piece of legislation,<ref>{{cite book |title = Evolution of the Great Lakes Water Quality Agreement |first1 = Paul |last1 = Muldoon |first2 = Lee |last2 = Botts |publisher = Michigan State University Press |year = 2005 }}</ref> along with the bi-national [[Great Lakes Water Quality Agreement]] signed by Canada and the U.S. A variety of steps taken to process industrial and municipal pollution discharges into the system greatly improved water quality by the 1980s, and Lake Erie in particular is significantly cleaner.<ref>{{cite web |url = http://www.michigan.gov/dnr/0%2C1607%2C7-153--145852--%2C00.html |archive-url = https://web.archive.org/web/20130830182201/http://www.michigan.gov/dnr/0%2C1607%2C7-153--145852--%2C00.html |archive-date = August 30, 2013 |title = Recovery of Lake Erie Walleye a Success Story |publisher = Michigan Department of Natural Resources |date = June 8, 2006 }}</ref> Discharge of toxic substances has been sharply reduced. Federal and state regulations control substances like [[Polychlorinated biphenyl|PCBs]]. The first of 43 "[[Great Lakes Areas of Concern]]" to be formally "de-listed" through successful cleanup was Ontario's Collingwood Harbour in 1994; Ontario's Severn Sound followed in 2003.<ref>{{cite web |work = binational.net |url = http://binational.net/ourgreatlakes/ourgreatlakes.pdf |archive-url = https://web.archive.org/web/20051227162745/http://binational.net/ourgreatlakes/ourgreatlakes.pdf |archive-date = December 27, 2005 |title = Our Great Lakes }}</ref> [[Presque Isle Bay]] in Pennsylvania is formally listed as in recovery, as is Ontario's Spanish Harbour. Dozens of other Areas of Concern have received partial cleanups such as the [[River Rouge (Michigan)|Rouge River (Michigan)]] and Waukegan Harbor (Illinois).<ref>{{cite web |url = http://www.epa.state.il.us/environmental-progress/v22/n1/waukegan-harbor.html |archive-url = https://web.archive.org/web/20141129040321/http://www.epa.state.il.us/environmental-progress/v22/n1/waukegan-harbor.html |archive-date = November 29, 2014 |title = Milestone in Waukegan Harbor PCB Cleanup |publisher = Illinois Environmental Protection Agency |date = Spring 1997 }}</ref>

Phosphate detergents were historically a major source of nutrient to the Great Lakes algae blooms in particular in the warmer and shallower portions of the system such as Lake Erie, [[Saginaw Bay]], [[Green Bay (Lake Michigan)|Green Bay]], and the southernmost portion of Lake Michigan. By the mid-1980s, most jurisdictions bordering the Great Lakes had controlled phosphate detergents.<ref>{{cite web |last = Knud-Hansen |first = Chris |date = February 1994 |url = http://www.colorado.edu/conflict/full_text_search/AllCRCDocs/94-54.htm |title = Historical Perspective of the Phosphate Detergent Conflict |archive-url = https://web.archive.org/web/20100528155811/http://www.colorado.edu/conflict/full_text_search/AllCRCDocs/94-54.htm |archive-date = May 28, 2010 |id = Working Paper 94-54 |via = Colorado.edu |access-date = December 7, 2016 }}</ref> Blue-green algae, or [[cyanobacteria]] blooms,<ref>{{cite web |url = https://www.weather.gov/cle/LakeErieHAB |title = Lake Erie Harmful Algal Bloom |publisher = National Weather Service }}</ref> have been problematic on Lake Erie since 2011.<ref>{{cite news |url = https://www.nytimes.com/2013/03/15/science/earth/algae-blooms-threaten-lake-erie.html |title = Spring Rain, Then Foul Algae in Ailing Lake Erie |date = March 14, 2013 |work = The New York Times }}</ref> "Not enough is being done to stop fertilizer and phosphorus from getting into the lake and causing blooms," said Michael McKay, executive director of the Great Lakes Institute for Environmental Research (GLIER) at the [[University of Windsor]]. The largest Lake Erie bloom to date occurred in 2015, exceeding the severity index at 10.5 and in 2011 at a 10.<ref name="windsorstar.com">{{cite news |url = https://windsorstar.com/news/local-news/large-lake-erie-algal-bloom-nearing-colchester-tested-for-toxicity |archive-url = https://web.archive.org/web/20190811140408/https://windsorstar.com/news/local-news/large-lake-erie-algal-bloom-nearing-colchester-tested-for-toxicity |archive-date = August 11, 2019 |title = Large Lake Erie algal bloom nearing Colchester tested for toxicity |work = Windsor Star |date = August 7, 2019 |first = Sharon |last = Hill |access-date = August 12, 2019 }}</ref> In early August 2019, satellite images depicted a bloom stretching up to 1,300 square kilometers on Lake Erie, with the heaviest concentration near [[Toledo, Ohio]]. A large bloom does not necessarily mean the cyanobacteria ... will produce toxins", said Michael McKay, of the University of Windsor. Water quality testing was underway in August 2019.<ref>{{cite news |url = http://www.uwindsor.ca/dailynews/2019-08-07/uwindsor-researchers-test-waters-harmful-algae-bloom |archive-url = https://web.archive.org/web/20190812145246/http://www.uwindsor.ca/dailynews/2019-08-07/uwindsor-researchers-test-waters-harmful-algae-bloom |archive-date = August 12, 2019 |title = UWindsor researchers test the waters for harmful algae bloom }}</ref><ref name="windsorstar.com" />

==== Mercury ====
Until 1970, [[Mercury (element)|mercury]] was not listed as a harmful chemical, according to the United States Federal Water Quality Administration. In the 21st century, mercury has become more apparent in water tests. Mercury compounds have been used in paper mills to prevent slime from forming during their production, and chemical companies have used mercury to separate chlorine from brine solutions. Studies conducted by the [[United States Environmental Protection Agency|Environmental Protection Agency]] have shown that when the mercury comes in contact with many of the bacteria and compounds in the fresh water, it forms the compound [[Methylmercury|methyl mercury]], which has a much greater impact on human health than elemental mercury due to a higher propensity for absorption. This form of mercury is not detrimental to a majority of fish types, but is very detrimental to people and other wildlife animals who consume the fish. Mercury has been known for health related problems such as birth defects in humans and animals, and the near extinction of eagles in the Great Lakes region.<ref>{{cite web |url = http://www.idph.state.il.us/envhealth/factsheets/mercuryspills.htm |title = Mercury Spills |publisher = Idph.state.il.us |access-date = February 19, 2011 }}</ref>

==== Sewage ====
The amount of raw sewage dumped into the waters was the primary focus of both the first Great Lakes Water Quality Agreement and federal laws passed in both countries during the 1970s. Implementation of secondary treatment of municipal sewage by major cities greatly reduced the routine discharge of untreated sewage during the 1970s and 1980s.<ref>{{cite web |url = http://ohioseagrant.osu.edu/_documents/publications/FS/FS-046%20Lake%20Erie%20water%20quality%20past%20present%20future.pdf |archive-url = https://web.archive.org/web/20060902100228/http://ohioseagrant.osu.edu/_documents/publications/FS/FS-046%20Lake%20Erie%20water%20quality%20past%20present%20future.pdf |archive-date = September 2, 2006 |url-status = live |title = Lake Erie Water Quality Past Present and Future |access-date = December 4, 2013 }}</ref> The [[International Joint Commission]] in 2009 summarized the change: "Since the early 1970s, the level of treatment to reduce pollution from waste water discharges to the Great Lakes has improved considerably. This is a result of significant expenditures to date on both infrastructure and technology, and robust regulatory systems that have proven to be, on the whole, quite effective."<ref name="ijc.org">{{Cite book |url = http://www.ijc.org/php/publications/pdf/ID1631.pdf |archive-url = https://web.archive.org/web/20100924165650/http://ijc.org/php/publications/pdf/ID1631.pdf |archive-date = September 24, 2010 |url-status = live |title = 14th Biennial Report on Great Lakes Water Quality }}</ref> The commission reported that all urban sewage treatment systems on the U.S. side of the lakes had implemented secondary treatment, as had all on the Canadian side except for five small systems.{{Citation needed|date=September 2012}}

Though contrary to federal laws in both countries, those treatment system upgrades have not yet eliminated [[combined sewer]] overflow events.{{citation needed|date=December 2013}} This describes when older sewerage systems, which combine storm water with sewage into single sewers heading to the treatment plant, are temporarily overwhelmed by heavy rainstorms. Local sewage treatment authorities then must release untreated effluent, a mix of rainwater and sewage, into local water bodies. While enormous public investments such as the [[Deep Tunnel]] projects in Chicago and [[Milwaukee]] have greatly reduced the frequency and volume of these events, they have not been eliminated. The number of such overflow events in Ontario, for example, is flat according to the International Joint Commission.<ref name="ijc.org"/> Reports about this issue on the U.S. side highlight five large municipal systems (those of Detroit, Cleveland, Buffalo, Milwaukee and [[Gary, Indiana|Gary]]) as being the largest current periodic sources of untreated discharges into the Great Lakes.<ref>{{cite web |url = http://healthylakes.org/press-releases/new-report-solving-region%E2%80%99s-sewage-crisis-will-create-jobs-restore-great-lakes/ |title = New Report: Solving Region's Sewage Crisis Will Create Jobs, Restore Great Lakes |archive-url = https://web.archive.org/web/20141129035802/http://healthylakes.org/press-releases/new-report-solving-region%E2%80%99s-sewage-crisis-will-create-jobs-restore-great-lakes/ |archive-date = November 29, 2014 |work = Healthylakes.org |date = August 9, 2010 |access-date = December 7, 2016 }}</ref>
[[File:Diatoms_through_the_microscope.jpg|thumb|upright=1.3|Diatoms of different sizes seen through the microscope. These minuscule [[phytoplankton]] are encased within a [[silicate]] [[cell wall]].]]

The fish of the Great Lakes have anti-depressant drugs meant for humans in their brains, which has caused concerns. The number of American adults who take anti-depressant drugs rose from 7.7% of all American adults in 1999–2002 to 12.7% in 2011–2014. As the anti-depressant drugs pass out of human bodies and through sanitation systems into the Great Lakes, this has resulted in fish in the Great Lakes with twenty times the level of anti-depressants in their brains than what is in the water, leading to the fish being exceedingly happy and hence less risk-averse, to the extent of damaging the fish populations.<ref name="The Economist">{{cite news |title = Antidepressants are finding their way into fish brains |url = https://www.economist.com/united-states/2018/02/08/antidepressants-are-finding-their-way-into-fish-brains |access-date = January 15, 2023 |newspaper = The Economist |date = February 8, 2018 }}</ref>

==== Plastic ====
Researchers have found that more than {{convert|22|e6lb}} of plastic end up in the Great Lakes each year.<ref name=agl>{{cite web |title = Great Lakes Plastic Pollution |url = https://greatlakes.org/great-lakes-plastic-pollution-fighting-for-plastic-free-water/ |access-date = April 21, 2023 |publisher = Alliance for the Great Lakes |language = en-US }}</ref> Plastics in the water break up into very small particles known as [[microplastics]]. Microplastics can also come from synthetic clothing washed down our drains.<ref name=varsity>{{cite news |first = Nicole |last = Szabo |date = September 5, 2021 |title = U of T researchers discover microplastics in all samples of Great Lakes fish |url = https://thevarsity.ca/2021/09/04/ontario-freshwater-microplastics-lakes/ |access-date = April 21, 2023 |website = The Varsity |language = en-US }}</ref> [[Plastic waste]] found in the lakes include [[single-use plastic]]s, plastics used in packaging, takeout containers as well as [[Plastic pellet pollution|pre-production pellets]] produced by [[plastics industry]].<ref>{{cite news |first1 = Inayat |last1 = Singh |first2 = Alice |last2 = Hopton |date = October 1, 2021 |title = Industrial plastic is spilling into Great Lakes, and no one's regulating it, experts warn |publisher = CBC News |url = https://www.cbc.ca/news/science/plastics-waste-great-lakes-water-1.6185621 |access-date = April 21, 2023 }}</ref> High concentrations of microplastics were discovered in 100 percent of the fish that were studied by researchers from the Rochman Lab. About {{convert|50|e6lb}} of fish is harvested each year from Great Lakes which has raised concerns on how this might affect human health.<ref name=varsity/> Microscopic pieces of plastic have also been found in drinking water coming from Great Lakes. It is estimated that nearly 40 million people in the region rely on drinking water from the Great Lakes.<ref name=agl/>

A number of self-operating floating devices called Seabin, were put in the Great Lakes to capture plastic trash as part of the Great Lakes Plastic Cleanup project. The project captured 74,000 pieces of trash using this technology between 2020 and 2021; however, it does not claim to catch up with {{convert|22|e6lb}} of plastic that ends up in Great Lakes every year. The production, consumption, and throwing away of plastics seems to remain the core of Great Lakes trash problem.<ref>{{Cite web |last = Redelmeier |first = Rebecca |date = October 14, 2022 |title = How a fleet of robots could help solve the Great Lakes plastic pollution problem |url = https://www.theverge.com/2022/10/14/23401381/great-lakes-plastic-pollution-cleanup-tech-robots |access-date = April 21, 2023 |website = The Verge |language = en-US }}</ref>

=== Impacts of climate change on algae ===
Algae such as [[diatom]]s, along with other [[phytoplankton]], are [[photosynthetic]] [[primary producers]] supporting the [[food web]] of the Great Lakes,<ref>{{cite web |url = https://www.glc.org/lakes/ |title = About the Lakes |publisher = Great Lakes Commission }}</ref> and have been [[Effects of global warming|affected by global warming]].<ref>{{cite web |url = https://greatlakesecho.org/2019/02/13/monitoring-algal-blooms-in-the-great-lakes-basin/ |title = Monitoring algal blooms in the Great Lakes Basin |first = Kurt |last = Williams |date = February 13, 2019 |website = Great Lakes Echo }}</ref> The changes in the size or in the function of the primary producers may have a direct or an indirect impact on the food web. Photosynthesis carried out by diatoms constitutes about one fifth of the total photosynthesis.{{Where|date=February 2021}} By taking {{CO2 |link=yes}} out of the water to photosynthesize, diatoms help to stabilize the [[pH]] of the water, as {{CO2}} would react with water to produce [[Carbon dioxide#In aqueous solution|carbonic acid]]. 
:{{chem2|CO2 + H2O <-> HCO3- + H+}}
Diatoms acquire [[Inorganic compound|inorganic]] carbon through passive diffusion of {{CO2}} and [[Bicarbonate|{{chem2|HCO3-}}]], and use [[carbonic anhydrase]] mediated active transport to speed up this process.<ref>{{cite journal |last1 =Burkhardt |first1 = Steffen |last2 = Amoroso |first2 = Gabi |last3 = Riebesell |first3 = Ulf |last4 = Sültemeyer |first4 = Dieter |date = September 2001 |title = CO<sub>2</sub> and {{chem|HCO|3|-}} uptake in marine diatoms acclimated to different CO<sub>2</sub> concentrations |journal =Limnology and Oceanography |volume = 46 |issue = 6 |pages = 1378–1391 |doi=10.4319/lo.2001.46.6.1378}}</ref> Large diatoms require more carbon uptake than smaller diatoms.<ref name=":0">{{cite journal |first1 = Brian N. |last1 = Popp |first2 = Edward A. |last2 = Laws |first3 = Robert R. |last3 = Bidigare |first4 = John E. |last4 = Dore |first5 = Kristi L. |last5 = Hanson |first6 = Stuart G. |last6 = Wakeham |journal = Geochimica et Cosmochimica Acta |year = 998 |title = Effect of Phytoplankton Cell Geometry on Carbon Isotopic Fractionation |volume = 62 |issue =  |pages = 69–77 |doi = 10.1016/S0016-7037(97)00333-5 }}</ref> There is a [[Correlation and dependence|positive correlation]] between the surface area and the chlorophyll concentration of diatom cells.<ref>{{cite journal |last = Durbin |first = E.G. |year = 1977 |title = Studies on the Autecology of the Marine Diatom ''Thalassiosira nordenskioeldii'' II. The Influence of Cell Size on Growth Rate, and Carbon, Nitrogen, Chlorophyll ''a'' and Silica Content |journal = Journal of Phycology |volume = 13 |issue = 2 |pages = 150–155 |doi = 10.1111/j.1529-8817.1977.tb02904.x |bibcode = 1977JPcgy..13..150D }}</ref>