Sediments deposited over the past 220,000 years in Bear Lake, Utah and Idaho, are predominantly calcareous silty clay, with calcite as the dominant carbonate mineral. The abundance of siliciclastic sediment indicates that the Bear River usually was connected to Bear Lake. However, three marl intervals containing more than 50% CaCO₃ were deposited during the Holocene and the last two interglacial intervals, equivalent to marine oxygen isotope stages (MIS) 5 and 7, indicating times when the Bear River was not connected to the lake. Aragonite is the dominant mineral in two of these three high-carbonate intervals. The high-carbonate, aragonitic intervals coincide with warm interglacial continental climates and warm Pacific sea-surface temperatures. Aragonite also is the dominant mineral in a carbonate-cemented microbialite mound that formed in the southwestern part of the lake over the last several thousand years. The history of carbonate sedimentation in Bear Lake is documented through the study of isotopic ratios of oxygen, carbon, and strontium, organic carbon content, CaCO₃ content, X-ray diffraction mineralogy, and HCl-leach chemistry on samples from sediment traps, gravity cores, piston cores, drill cores, and microbialites.

Sediment-trap studies show that the carbonate mineral that precipitates in the surface waters of the lake today is high-Mg calcite. The lake began to precipitate high-Mg calcite sometime in the mid–twentieth century after the artificial diversion of Bear River into Bear Lake that began in 1911. This diversion drastically reduced the salinity and Mg²⁺:Ca²⁺ of the lake water and changed the primary carbonate precipitate from aragonite to high-Mg calcite. However, sediment-trap and core studies show that aragonite is the dominant mineral accumulating on the lake floor today, even though it is not precipitating in surface waters. The isotopic studies show that this aragonite is derived from reworking and redistribution of shallow-water sediment that is at least 50 yr old, and probably older. Apparently, the microbialite mound also stopped forming aragonite cement sometime after Bear River diversion. Because of reworking of old aragonite, the bulk mineralogy of carbonate in bottom sediments has not changed very much since the diversion. However, the diversion is marked by very distinct changes in the chemical and isotopic composition of the bulk carbonate.

After the last glacial interval (LGI), a large amount of endogenic carbonate began to precipitate in Bear Lake when the Pacific moisture that filled the large pluvial lakes of the Great Basin during the LGI diminished, and Bear River apparently abandoned Bear Lake. At first, the carbonate that formed was low-Mg calcite, but ~11,000 years ago, salinity and Mg²⁺:Ca²⁺ thresholds must have been crossed because the amount of aragonite gradually increased. Aragonite is the dominant carbonate mineral that has accumulated in the lake for the past 7000 years, with the addition of high-Mg calcite after the diversion of Bear River into the lake at the beginning of the twentieth century.