Big Soda Lake is a 63 m deep, 1.6 km² maar lake in the Great Basin of Nevada, USA. Water level in the lake is controlled by groundwater inputs from the surrounding aquifer and the only surface water input is rainfall, which is negligible. A core taken in 2010 records an 8.75 m depositional history of the lake. A radiocarbon date on fossil pollen from 8.4 m below the sediment water interface (BSWI) of 14,740 (+1120/−825) cal yr BP suggests that the core may cover the latest Pleistocene and Holocene depositional history of the lake. Stable isotope values of oxygen and carbon (δ¹⁸O and δ¹³C) on authigenic calcite, diatom assemblages, and sedimentary structures all show consistent hydrological change from initially saline water at the bottom of the core to fresh/brackish water at about 6 m BWSI, back to saline water at 4.3 m. At 4.3 m depth, the bedding and color of the core change abruptly, and the stable- isotope and diatom assemblages indicate a consistently hypersaline lake until near the top of the core, when fresh water entered the lake due to irrigation and canal building in the twentieth century. The stable isotopes of the calcite abruptly change from inversely varying isotopic compositions below 4.3 m depth to covarying above. This break between relatively fresh and saline conditions in the lake occurs during the middle Holocene, although the exact timing of the transition is unknown due to variability in the ¹⁴C age determinations. The cause for such an abrupt change is difficult to explain through climate shifts, as evidence suggests climate in the Great Basin was different from what the Big Soda Lake record indicates in the Early Holocene. It is hypothesized that the Walker River flowed to the Carson River basin before 5600 cal yr BP, with water either flowing directly into the lake or raising the groundwater table sufficiently to freshen Big Soda Lake. The initial increase in salinity likely was caused by decreased flow of the Walker River due to Middle Holocene aridity. The lake level lowered slowly, and more saline conditions prevailed until 4.3 m depth when water from the Walker River stopped flowing into the Carson River basin. Above 4.3 m depth, diatom and isotopic evidence indicates that the lake became consistently saline. The isotopic and diatom assemblage transitions observed in Big Soda Lake sediment are not consistent with climate reconstructions and demonstrate that hydrologic shifts in a basin can be an important driver of change regardless of climatic conditions. However, climate shifts may also play a role in the hydrologic changes by supplying more or less water to river courses that may induce river avulsion.