The world-renowned middle Miocene Clarkia lacustrine deposits (15.4–16.0 Ma) in northern Idaho, United States, known as Fossil Lagerstätten, yield extraordinary fossils that preserve in situ ancient biomolecules and organic biomarkers. The sudden formation of the Clarkia Lake basin by means of the Columbia River Basalt damming the proto–St. Maries River is well documented, but less is known about the tempo and mode of the lake environmental succession which impacted on the preservation of these Fossil Lagerstätten. Here, we present evidence for a previously unrecognized, geologically instantaneous drop in the Clarkia Lake water level, using tetraether-based water-depth proxies from a continuous sedimentary sequence at the classic P-33 site. Terrestrial hydrological conditions inferred from compound-specific hydrogen isotope compositions (δD) and tetraether-derived temperature estimates from the same sequence show that the rapid shallowing by >10 m was independent of regional climatic changes. We hypothesize that a volcanic-related geological event was primarily responsible for the rapid reduction of Clarkia Lake water depth—an event that played a decisive role in switching depositional conditions for Clarkia Fossil Lagerstätten from a conservation deposit to a concentration deposit.