Isotopic compositions of lacustrine carbonates are commonly used for dating and paleoenvironmental reconstructions. Here we use carbonate δ13C and δ18O, clumped (Δ47), and 14C compositions to better understand the carbonate isotope system in closed-basin lakes and trace the paleohydrologic and temperature evolution in the Chewaucan closed-basin lake system, northern Great Basin, USA, over the Last Glacial/Holocene transition. We focus on shorezone tufas to establish that they form in isotopic equilibrium with lake water and DIC, they can be dated reliably using 14C, and their clumped isotope composition can be used to reconstruct past lake temperature. Calculations of the DIC budget and reservoir age for the lake indicate residence time is short, and dominated by exchange with atmospheric CO2 at all past lake levels. Modern lake DIC and shorezone tufas yield δ13C and 14C values consistent with isotopic equilibrium with recent fossil fuel and bomb-influenced atmospheric CO2, supporting these calculations. δ13C values of fossil tufas are also consistent with isotopic equilibrium with pre-industrial atmospheric CO2 at all shoreline elevations. This indicates that the 14C reservoir effect for this material is negligible. Clumped isotope (Δ47) results indicate shorezone tufas record mean annual lake temperature. Modern (average 13 ± 2 °C) and 18 ka BP-age tufas (average 6 ± 2 °C) have significantly different temperatures consistent with mean annual temperature lowering of 7 ± 3 °C (1 SE) under full glacial conditions. For shorezone tufas and other lake carbonates, including spring mounds, mollusk shells, and ostracod tests, overall δ13C and δ18O values co-vary according to the relative contribution of spring and lacustrine end member DIC and water compositions in the drainage system, but specific isotope values depend strongly upon sample context and are not well correlated with past lake depth. This contrasts with the interpretation that carbonate isotopes in closed-basin lake systems reflect changes in DIC and water budgets connected to higher or lower lake volumes. Instead, a small overlapping range of isotope compositions characterize multiple lake levels, so that none can be identified uniquely by isotope composition alone. Relative to other lake carbonates, δ13C and δ18O values for ostracods in Ana River Canyon deposits are very strongly influenced by Ana River water, suggesting low lake level and volume characterized Summer Lake for most of the past 100,000 years. Coupled with sedimentologic observations, the Ana River deposits thus suggest dry conditions like today are close to the mean climate state in the northern Great Basin. By contrast, basin-integrating highstands such as that dating to ∼14 ka BP, during the last glacial termination, are hydrologically unique and short-lived. Overall, our results indicate carbonate isotope records must account for the specific geochemical and hydrologic characteristics of lake system in order to provide robust paleoenvironmental reconstructions.