The limnology of the lake shows it contains approximately 280 million tons of dissolved salts, with the salinity varying depending upon the amount of water in the lake at any given time. Before 1941, average salinity was approximately 50 grams per liter (g/L) (compared to a value of 31.5 g/L for the world's oceans). In January 1982, when the lake reached its lowest level of , the salinity had nearly doubled to 99 g/L. In 2002, it was measured at 78 g/L and is expected to stabilize at an average 69 g/L as the lake replenishes over the next 20 years.
An unintended consequence of ending the water diversions was the onset of a period of "meromixis" in Mono Lake. In the time prior to this, Mono Lake was typically "monomictic"; which means that at least once each year the deeper waters and the shallower waters of the lake mixed thoroughly, thus bringing oxygen and other nutrients to the deep waters. In meromictic lakes, the deeper waters do not undergo this mixing; the deeper layers are more saline than the water near the surface, and are typically nearly devoid of oxygen. As a result, becoming meromictic greatly changes a lake's ecology.
Mono Lake has experienced meromictic periods in the past; this most recent episode of meromixis, brought on by the end of the water diversions, commenced in 1994 and had ended by 2004.