Small sub-alpine glacial lakes are often targeted as Holocene paleoclimate archives, but their evolution as landforms and depositional basins is understudied. At June Lake in the eastern Sierra Nevada of California (USA), bathymetry, surface sediment composition, and seismic stratigraphy are studied to assess the modern sedimentary system and gain insight into the basin's origins. A basin-wide seismic survey reveals sublacustrine morphological features that attest to the role of ice in scouring the June Lake basin, including a prominent abraded bedrock shoal and an adjacent overdeepened depression. The seismic survey reveals four acoustically distinct stratigraphic units that reflect the history of sedimentation following glacial scouring. The youngest of these is represented in the recovered lacustrine core records as hemipelagically deposited, organic-rich, laminated diatomaceous oozes alternating with coarse tephra beds. The organic-rich oozes are characterized by low carbon and nitrogen stable-isotope values and occur in profundal areas of the modern lake floor. These sediments suggest an algae-dominated productivity regime and preservation of organic matter at depth. With no perennial streams entering June Lake, surface-sediment grain-size distribution and geochemistry are controlled by water depth and basin morphology. Additional modern facies types include poorly sorted coarse detrital landslide deposits below steep basin walls and volcaniclastic sandy gravel in windward littoral areas. These data provide a modern facies model for sedimentation in ice-scoured, hydrologically closed sub-alpine lakes and a baseline for future paleoclimate studies using June Lake sediment cores.