Green Lake and its sister Round Lake, are a pair of unique bodies of water located in the aboriginal territory of the Onandoga nation. This writeup will concern itself with Green Lake, but much of this information carries over to its sister.
The final remnants of a plunge pool formed during the last ice age by a glacial waterfall at least twice the size of Niagara Falls; Green Lake is situated in a gorge and fed entirely by rain and groundwater. As a result, it is one of the few meromictic lakes on earth.
So, okay, in general terms, lakes do this:

For the warmer months water organizes into distinct layers, each circulating in their own way. The warmest water, being the least dense, sits at the top. This is where the phytoplankton hang out, producing oxygen and consuming nutrients. The coldest water, being the most dense, sits at the bottom. This is where nutrients tend to accumulate and oxygen gets depleted by animal life. As summer turns to winter the top layers get colder and the water mixes as stratification breaks down, the same happens as winter turns back to summer. This process helps more evenly distribute oxygen and nutrients.
Ok so Green Lake doesn't do this.
The bottom of the lake is totally devoid of oxygen, so no decomposition; whatever falls down there, stays down there. The water is also very high in mineral content, which leaves layers of calcite deposits on anything that isn't moving. Moreover there is a layer of bacterially active water around 18-20 meters down that makes the water purple at that specific depth. Thanks to photosynthetic bacteria that deposit some of the minerals in the water, Green Lake is home to one of the few existing freshwater reefs.

I just think its neat.
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Gotta be honest, I had no idea lakes did that. But it's cool as hell.
Am I right in assuming that the seperation of a single cycle into an epilimnion and hypolimnion is dependent on the thermal gradient of the water?
The hotter water up top moves faster, and when currents try to move downwards, they are "reflected" if they encounter a large thermal gradient (just like how light reflects when it encounters a new medium).
So if you have a really large thermal gradient, you can actually get more layers of cycles?
I asked a researcher about this and the answer is basically no, more or less. While the kind of stratification shown in the diagram in the main post is highly simplified, it can still be broken up into three main layers in terms of temperature and density. The coldest water at the bottom, the warmest at the top, and a slowly mixing layer between them.
The image below is a cross section of lake Ontario in late summer, the hypolimnion in blue, the metalimnion/thermocline is somewhere in the bottom of the green section, and the epilimnion is the red and most of the green.
The other image below is a graph showing temperature at depth over time, the parts in May and October where it is all one color represent mixing events when the temperature difference between the layers is not enough to enforce stratification.
I see. Thanks for the response!
That lake thermal structure is quite interesting.
So as the temperature/wind speed is raised, the epilimnion just becomes bigger until everything is just one layer.
Or is it more a function of time? It takes months for the hypolimnion to mix and heat?