Fitting a pre-established region-specific Parallel Factor Analysis (PARAFAC) model to new dissolved organic matter (DOM) samples has become a popular approach in DOM studies. A key step during the development of the pre-established model is to identify the fluorescence fingerprint, i.e. the number of fluorescent DOM (FDOM) components as well as their excitation and emission spectral features. In practice the samples to use for model development may not be measured immediately after sampling and will instead be stored for a relatively long time, thus raising the question whether the storage would change the intrinsic fingerprints. In this study, two PARAFAC models were separately developed and validated for the same set of surface water DOM samples from an estuary and its river, immediately after sampling and after 9-month storage respectively. The fingerprint did not change after storage, regardless of the change of the intensity of some components. The findings in this study highlighted that DOM samples stored using a simple protocol (i.e. filtration to 0.45 μm pore size without any preservatives and placed at 4 °C in the dark under airtight conditions) for a few months would not change fluorescence fingerprints for PARAFAC and broaden our understanding of the application of PARAFAC to DOM studies.