Changes in diatom fossil assemblages from lake sediment cores indicate variations in hydrologic and climatic conditions at Bear Lake (Utah-Idaho) during the late glacial and Holocene. From 19.1 to 13.8 cal ka there is an absence of well-preserved diatoms because prolonged ice cover and increased turbidity from glacier-fed Bear River reduced light and limited diatom growth. The first well-preserved diatoms appear at 13.8 cal ka. Results of principal components analysis (PCA) of the fossil diatom assemblages from 13.8 cal ka to the present track changes related to fluctuations of river inputs and variations of lake levels. Diatom abundance data indicate that the hydrologic balance between 13.8 and 7.6 cal ka is strongly tied to river inputs, whereas after 7.6 cal ka the hydrologic balance is more influenced by changes in lake evaporation. Wet conditions maintained high river inputs from 13.8 to 10.8 cal ka and from 9.2 to 7.6 cal ka, with a dry interval between 10.8 and 9.2 cal ka. After 9.2 cal ka until 2.9 cal ka lake levels were high except for two periods, one between 7.6 and 5.8 cal ka and one between 4.3 and 3.8 cal ka, as a result of decreased effective moisture. After 2.9 cal ka, fossil diatom assemblages suggest drier conditions until 1.6 cal ka to the present, when fragments of large, pennate diatoms appear, possibly the result of a rapid lake transgression. Although similarities exist between the Bear Lake records and other western hydrologic and climatic records, the covariations are not strong. Our data suggest that climatic regimes at Bear Lake have changed frequently over time, perhaps as a consequence of the position of several important climatic boundaries near Bear Lake.