The Big Lost trough is an upper Pliocene to Holocene sedimentary basin containing volcanic sills in the northeastern Snake River Plain, Idaho. The basin receives sediment primarily from Basin and Range fluvial systems of the Big Lost River, Little Lost River, and Birch Creek. The Big Lost trough contains a >200-m-thick succession of lacustrine, fluvial, eolian, and playa sediments, recording high-frequency Quaternary climatic fluctuations interbedded with basalt flows. Alternating deposition of clay-rich lacustrine sediments and sandy fluvial and eolian sediments in the central part of the basin was in response to the interaction of fluvial and eolian systems with Pleistocene Lake Terreton. The source areas for modern sands from the fluvial systems can be differentiated by using both petrography and U/Pb age spectra from detrital-zircon populations. Provenance data from subsurface sands indicate that the Big Lost trough was supplied with sand largely deposited by the Big Lost River, with local redeposition by eolian processes, similar to the modern depositional system. Provenance and stratigraphic data suggest that during Pleistocene wet climate cycles, the center of the basin was dominated by lacustrine sedimentation; during dry climate cycles, the base level dropped, the Big Lost River prograded across the basin, and the eolian system became active. At least seven climate oscillations are recorded in strata deposited between ∼140 and ∼1250 ka.