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Marine dissolved organic matter (DOM) contains a complex mixture of small molecules that eludes rapid biological degradation. Spatial and temporal variations in the abundance of DOM reflect the existence of fractions that are removed from the ocean over different time scales, ranging from seconds to millennia. However, it remains unknown whether the intrinsic chemical properties of these organic components relate to their persistence. Here, we elucidate and compare the molecular compositions of distinct DOM fractions with different lability along a water column in the North Atlantic Gyre. Our analysis utilized ultra high resolution Fourier transform ion cyclotron resonance mass spectrometry at 21 T coupled to liquid chromatography and a novel data pipeline developed in CoreMS that generates molecular formula assignments and metrics of isomeric complexity. Clustering analysis binned 14 857 distinct molecular components into groups that correspond to the depth distribution of semilabile, semirefractory, and refractory fractions of DOM. The more labile fractions were concentrated near the ocean surface and contained more aliphatic, hydrophobic, and reduced molecules than the refractory fraction, which occurred uniformly throughout the water column. These findings suggest that processes that selectively remove hydrophobic compounds, such as aggregation and particle sorption, contribute to variable removal rates of marine DOM.