We investigated relationships among modern diatom species composition and physical and chemical characteristics of high-elevation lakes of the Sierra Nevada (California), to develop transfer functions that can be used to infer historic lake conditions. Data were collected from 50 lakes in National Parks and Forests of the central and southern Sierra Nevada. Multivariate statistical methods revealed that acid neutralizing capacity (ANC) and nitrate accounted for significant variation in diatom taxa. A training set with 242 modern diatom taxa from a subset of 41 lakes was used to develop transfer functions for ANC and nitrate using weighted averaging techniques. ANC and nitrate calibration ranges were 23.0–137 μEq/L and 0.18–9.5 μM, respectively. Coefficients of determination for the models were: ANC: R2 = 0.76, and Rjackknife2 = 0.44; NO3: R2 = 0.67, and Rjackknife2 = 0.27. The ANC model was applied to the top 50 cm of sediments in Moat Lake to reconstruct ANC from ca. AD 350 to 2005. The reconstruction suggests that ANC declined by about 40 % (101–60 μEq/L) between the 1920s and the 1960s and then recovered to pre-1920s levels during 1980–2000. The magnitude of this ANC excursion was the largest observed during the past 1,600 years. We hypothesize that temporal variations in ANC were influenced by: (1) changes in rates of acid deposition, especially nitric acid and (2) variations in the timing and magnitude of snowmelt runoff.