Advancing our understanding of the behaviour of dissolved organic matter (DOM) in aquatic environments necessitates efforts to combine complementary analytical data sets. However, some analytical measurements require sample pre-treatment, while others are carried out on bulk water samples, and it remains unclear if the resulting data sets can be compared. Here, we investigated the impact of solid-phase extraction with PPL resins on DOM optical properties. In samples from contrasting Arctic fjords, extraction efficiencies based on optical properties varied spectrally with averages between 31 ± 13% at 411 nm and 40 ± 12% at 363 nm for chromophoric DOM. Similarly, the extraction efficiency for specific fluorescence components varied between 37 ± 16% and 58 ± 18%. Solid-phase extraction also decreased S275–295, fluorescence index, and the freshness index, but increased S350–400, and apparent fluorescence quantum yields, indicating that the extraction process was qualitatively selective. Six fluorescence components identified independently in bulk water samples and extracted DOM using parallel factor analysis exhibited different behaviours. Three had identical spectral properties before and after extraction, although their extraction efficiencies varied with water mass characteristics and DOM composition, whereas three other components appeared to change after extraction. With the exception of one fluorescence component, the dynamics of optical properties in bulk water samples were not accurately reflected by DOM extracts. These results indicate that solid-phase extraction imparts a qualitative selectivity that leads to the homogenization of DOM extracts relative to their original samples. Efforts to integrate chemical information from different analytical methods should prioritize comparisons of measurements obtained on the same samples.