We report the use of condensed phase–membrane introduction mass spectrometry as a novel method for the determination of acid dissociation constants for hydrophobic organic acids in aqueous solution at nanomolar concentrations. The technique is based on the pH‐dependent permeation of analytes through a semipermeable polydimethylsiloxane membrane probe that is immersed directly in aqueous samples. We describe the method and report the dissociation constant (pKa) values for compounds of biological and environmental relevance, including contaminants, pharmaceuticals, and naphthenic acids. The approach can be applied to individual compounds, combined suites, and complex mixtures at parts‐per‐billion levels. We report pKa values for 10 carboxylic acids with precision estimates and relative errors (where reliable literature values are available) of <0.1 log units. We report acidity constants for 2‐methyl‐3‐methoxy‐4‐phenyl butanoic acid (a biomarker for microcystin algal toxins) and 4‐t‐butylcyclohexane carboxylic acid (a model naphthenic acid) as 4.28 ± 0.03 and 5.15 ± 0.05, respectively. Furthermore, we employ this approach to measure the effect of both temperature and deuterium oxide (heavy water) on acid dissociation, reporting the enthalpy and entropy changes for the ionization of a representative carboxylic acid and substituted phenol. Environ Toxicol Chem 2019;38:1879–1889. © 2019 SETAC.