The limnology of Lake Michigan has changed dramatically since the late Pleistocene in response to the expansion and contraction of continental glaciers, to differential isostatic rebound, and to climate change. The lake sediment's stratigraphic trends, magnetic susceptibility, δ¹⁸O, and ostracode species abundance ratios provide criteria to identify the lake's response to glacial ice and to differential isostatic rebound. The latter phenomena dominate the lake's late Pleistocene and early Holocene history. The lake's hydrological budget provides the primary linkage between the lake and climate, particularly effective moisture. Dissolved salts were stored in the lake's water column when the lake's output shifted toward evaporation, but were flushed when output shifted toward outflow. The lake's salt storage history may be interpreted from some ostracode, δ¹⁸O, and magnetic susceptibility records found in sediment cores. Climate change influenced the entire lake's limnological history, but became the primary limnological driver from about the middle-Holocene to the present. The complex limnological history of Lake Michigan resulted in substantial changes in the ostracode species assemblages; from about 12,000 ka to about 5,500 ka, five ostracode intervals can be identified. These ostracode intervals provide a within-lake biostratigraphy and a stratigraphic reference for reconstruction of the paleoenvironmental dynamics of the lake.