Lake Coyote, California, which formed in one of five basins along the Mojave River, acted both as a part of the Lake Manix basin and, after the formation of Afton Canyon and draining of Lake Manix ca. 24.5 calibrated (cal) ka, a side basin that was filled episodically for the next 10,000 yr. As such, its record of lake level is an important counterpart to the record of the other terminal basin, Lake Mojave, following the draining of Lake Manix. We studied lake and fluvial deposits and their geomorphology and identified five principal periods of recurring lakes in the Coyote basin by dating mollusks. Several of these periods in detail consist of multiple lake-rise pulses, for which we identified specific fluvial deposits that represent the Mojave River entering the basin. The pulsed record of rapid lake rise and decline is interpreted as switching of the Mojave River between Lake Coyote and Lake Mojave. A composite lake record for both basins shows nearly continuous lake maintenance by the Mojave River from 24.5 cal ka to ca. 14 cal ka. One potential gap in the lake record, ca. 22.7–21.8 cal ka, may indicate either temporary river routing to yet another basin or a dry climatic period. The Mojave River discharge was sufficient to maintain at least one terminal lake throughout most of the Last Glacial Maximum and deglacial periods, indicating that paleoclimate was moist and/or cool well into the Bølling-Allerød and that the lake records may not be sensitive to variations from moderate to high discharge. Nuances of lake-level changes in both the Coyote and Mojave basins are difficult to interpret as paleoclimatic events because the current chronologic control on lake levels from nearshore deposits does not provide the necessary precision.