It is commonly thought that the climate conditions that supported lakes over a period of years in the Mojave Desert in southern California, only existed before 8,000 yr BP and that the environment has been arid since. Here we look at a drill core in the Silver Lake playa at the terminus of the Mojave River and find Holocene lake deposits which indicate that shallow lakes existed for at least a few decades. These deposits were radiocarbon dated at 3620 ±70 and 390 ± 90 yr BP, corresponding to the early Neo-glacial and the ‘little ice age’ respectively. To identify the conditions necessary to produce these Holocene lake events we have examined the modern climate and hydrological patterns that produce ephemeral lakes in this usually arid watershed. Available data indicate that there is a link between anomalous winter atmospheric conditions over the North Pacific and Mojave River floods that produced ephemeral lakes in the Silver Lake playa and that the Mojave River filters out small to medium floods and allows only the extreme floods to reach the terminal playa and leave a record of the anomalous conditions. We suggest that the late Holocene lakes may have resulted from persistent similar atmospheric circulation patterns and winter floods.