<jats:p>Abstract. Stable isotope data from lipid biomarkers and diatom silica recovered from lake sediment cores hold great promise for paleoclimate and paleohydrological reconstructions. However, these records rely on accurate calibration with modern precipitation and hydrologic processes and only limited data exist on the controls on the δD values for n-alkanoic acids from plant leaf waxes. Here we investigate the stable isotopic composition of modern precipitation, streams, lake water and ice cover, and use these data to constrain isotope systematics of the Lake El'gygytgyn Basin hydrology. Compound-specific hydrogen isotope ratios determined from n-alkanoic acids from modern vegetation are compared with modern precipitation and lake core top sediments. Multi-species net (apparent) fractionation values between source water (precipitation) and modern vegetation (e.g., &amp;amp;varepsilon;wax/precip mean value is −107 ± 12‰) agree with previous results and suggest a consistent offset between source waters and the δD values of alkanoic acids. We conclude that although there may be some bias towards a winter precipitation signal, overall δD values from leaf wax n-alkanoic acids record annual average precipitation within the El'gygytgyn Basin. A net fractionation calculated for 200-yr-integrated lake sediments yields &amp;amp;varepsilon;30/precip = −96 ± 8‰ and can provide robust net "apparent" fractionation to be used in future paleohydrological reconstructions. </jats:p>