Dissolved organic matter (DOM) is omnipresent in natural waters and is commonly incorporated into carbonates. Records of DOM from speleothems (secondary carbonates found in caves) have often been interpreted to reflect groundwater DOM concentrations. However, the fidelity of these records is largely untested. An understanding of the relationship between dripwater and speleothem DOM is thus required to allow speleothems to be reliably used as archives of DOM concentration. We precipitated calcite (CaCO3) crystals from weak solutions of (NH4)2CO3, CaCl2 and NH4Cl. These solutions also contained peat DOM (from 0 to 15 mgC/L). Fluorescence 3D excitation-emission matrix (3D EEM) analysis showed a strong, positive correlation between [DOM] in the parent-solution, and [DOM] in the calcite. Calcite precipitation was reduced at high DOM concentrations, potentially indicating inhibition of crystallisation. Partition coefficient values showed that DOMaq was subtly preferentially incorporated into calcite. Scanning electron microscope images indicated that the crystal structures were heavily influenced by DOM adsorption with finer, smooth-faced, rhombohedral crystals forming in growth solutions with low aqueous [DOM] (0–5 mgC/L), and prismatic, ‘impure’ crystals produced at high aqueous [DOM] (10 and 15 mgC/L). Overall, our results indicate that authigenic carbonates are likely to faithfully record variations in aqueous [DOM] within the natural range of DOM concentrations in representative freshwater systems (caves, soil water), and that crystal habits are altered by aqueous [DOM] within their growth solutions. We also applied our findings to three flowstones collected from three New Zealand caves which vary in climatic, vegetation and hydrological regimes. We conclude that differences in initial aqueous [DOM] do indeed control incorporation of DOM into calcite, and thus 3D EEM fluorescence can be used to reconstruct original aqueous [DOM] from authigenic carbonates.