Middle and late Holocene paleoclimate can be inferred from lake-level fluctuations recorded in the sediment of two, fresh, ground-water–controlled paleolakes in Lake Canyon, southeast Utah. The record from Lake Canyon contributes proxy climate data for the region as well as insight into climate controls on sedimentation. The paleolakes were formed immediately upcanyon of side-stream confluences where disproportionately large volumes of alluvium were focused into the bedrock canyon. Excellent exposure allows a depositional facies model to be developed and allostratigraphic units to be defined. A facies-based proxy for the past shoreline position is applied to the allostratigraphy and radiocarbon-based chronostratigraphy to produce a record of lake level through time that is corroborated by diatom proxy data. The earliest known lake formed during an episode of aggradation that began just before 5180 14C yr B.P., and an arroyo-cutting event drained the lake before 3050 14C yr B.P. The Lake Canyon record for the past 3 k.y. is composed of wet-dry cycles that have a periodicity of ∼520 yr, matching cycles resolved by the regional tree-ring record and the timing of the Medieval Warm Period and Little Ice Age. Lake level rose after 420 14C yr B.P. and aggradation continued until an advancing arroyo headcut drained the upper lake in a.d. 1915. Fluvial and lacustrine aggradation in Lake Canyon accompanied shifts to wetter climate when sediment stored in upper reaches of the drainage basin was delivered to the canyon, whereas arroyo cutting in the canyon is more a function of sediment supply and internal complex-response mechanisms than dry climate conditions. Correlation with other records is hindered by differences in resolution and the influence of local controls on alluvial stratigraphy. The Lake Canyon record confirms that episodes of high flood frequency in Holocene time have been wetter overall, but not all wet periods have been marked by high flood frequency.