This study presents a novel method for the analysis of low molecular weight (LMW) fatty acids in cave drip water and speleothems. The method development included optimization of sample preparation procedures, e.g., blank reduction, solid phase extraction, concentration of extracts as well as liquid chromatography coupled to electrospray ion-trap mass spectrometry (HPLC-ESI-IT/MS) measurement parameters. Retention times for five analytes (lauric acid, myristic acid, palmitic acid, stearic acid and arachidic acid) were between 5 and 13.5 min. Spiking experiments were performed to accomplish external calibrations which ranged from 12.5 to 75 ng per spiked water sample. The correlation coefficient ranged from 0.9558 to 0.9989. Inter-batch precision, expressed as the relative standard deviation of three replicates, was <7 %. Limits of detection ranged from 0.77 to 55.97 ng for the diverse analytes; obtained recoveries varied from 30 to 103 %. For a first application, cave drip water and stalagmite samples from Herbstlabyrinth-Adventhöhle cave system were analyzed. Concentrations ranged from 38.37 to 9,982.54 ng L(-1) for water samples and 2.52 to 1,344.96 ng g(-1) for the stalagmite. Thereby, the different fatty acids showed a distinctive variation. Whereas shorter-chained fatty acids exhibited similarities, arachidic acid showed opposite trends. Diverse correlations were found, which could improve the understanding of different organic sources of the lipids transported by drip water and preserved in speleothems. This new method provides a more selective extraction process, particularly adjusted to LMW fatty acids and therefore reduces the required sample size. Furthermore, it is applicable to stalagmite as well as cave drip water samples.