[2] The lake borders Madison on the north, east, and south, Middleton on the west, Shorewood Hills on the southwest, Maple Bluff on the northeast, and Westport on the northwest.

This was largely due to the Tenney Locks, which were constructed in 1849 to regulate shipping through the Madison Isthmus and led to a four-foot increase in the water level in Lake Mendota, submerging the beaches.

The degree of eutrophication was so high that in 1882, Edward Asahel Birge, a young zoologist and future president of the University of Wisconsin-Madison, documented Lake Mendota's first known toxic cyanobacterial blooms in conjunction with his collaborator Chancey Juday, marking the first step toward long-term studies of Lake Mendota.

This acquisition was part of a multi-million dollar flood mitigation effort led by Dane County Executive Joe Parisi dating back to 2019, when historic rains inundated creeks and caused the waters of Lake Monona to rise to their highest levels in over a century, that would allow Dane County to more efficiently move large volumes of water between the Madison lakes to avoid similar catastrophic impacts from flooding.

[23] In March 2021, researchers from the Center for Limnology concluded that climate change and the associated lengthening of summer weather have driven the annual formation of dead zones in Lake Mendota, which are oxygen-deficient layers deep in the water column.

These dead zones have been shown to remain in the lake for up to two months in the summer and have the potential to devastate the habitats of benthic fish.

In the absence of programs designed to mitigate climate change locally, the researchers indicated that the only way to reduce the frequency and severity of the dead zones is to limit the amount of fertilizer and nutrients that flow into Lake Mendota.

[24][25] On September 11, 2009, the invasive spiny water flea was discovered by the limnology class at the University of Wisconsin–Madison, making it the third known inland lake to harbor this species in Wisconsin.

A 2017 ecological survey of the Yahara lakes conducted by the Dane County Land & Water Resources Department found 24 aquatic plant species, including the coontail, muskgrass, common waterweed, small duckweed, American lotus, variable pondweed, wild celery, and common bladderwort.

Some of the bird species found in the Nature Preserve include the blue jay, American goldfinch, Baltimore oriole, bald eagle, great horned owl, marsh wren, and common loon.

Eutrophication has caused a rapid increase in the abundance of aquatic plants and in the frequency of harmful algal blooms, with the latter being attributable to cyanobacteria.

It was discovered by marine archeologist Tamara Thomsen and SCUBA assistant Mallory Dragt while joyriding on their scooters in June 2021.