Droughts in the western U.S. in the past 200 years are small compared to several megadroughts that occurred during Medieval times. We reconstruct duration and magnitude of extreme droughts in the northern Sierra Nevada from hydroclimatic conditions in Fallen Leaf Lake, California. Stands of submerged trees rooted in situ below the lake surface were imaged with sidescan sonar and radiocarbon analysis yields an age estimate of ∼1250 AD. Tree-ring records and submerged paleoshoreline geomorphology suggest a Medieval low-stand of Fallen Leaf Lake lasted more than 220 years. Over eighty more trees were found lying on the lake floor at various elevations above the paleoshoreline. Water-balance calculations suggest annual precipitation was less than 60% normal from late 10th century to early 13th century AD. Hence, the lake’s shoreline dropped 40–60 m below its modern elevation. Stands of pre-Medieval trees in this lake and in Lake Tahoe suggest the region experienced severe drought at least every 650–1150 years during the mid- and late-Holocene. These observations quantify paleo-precipitation and recurrence of prolonged drought in the northern Sierra Nevada.