Lynch-Stieglitz's research links the ocean and climate over the past 100,000 years. She has used carbon isotopes in benthic foraminifera to reconstruct air-sea exchange in carbon isotopes, changes in the movement of deep water masses, and Antarctic Intermediate Water in the transitions between glacial and interglacial periods. In the Atlantic Ocean, she has examined movement of the Gulf Stream during the Last Glacial Maximum and linked changes in the Atlantic meridional overturning circulation and to rapid changes in climate. Her research also extends to regions where ice alters the exchange of carbon dioxide between atmosphere and ocean in glacial periods, and work in the Pacific Ocean where she has examined sea surface temperatures from the Last Glacial Maximum to the present.