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Whether intrinsic molecular properties or extrinsic factors such as environmental conditions control the decomposition of natural organic matter across soil, marine and freshwater systems has been subject to debate^,,. Comprehensive evaluations of the controls that molecular structure exerts on organic matter’s persistence in the environment have been precluded by organic matter’s extreme complexity. Here we examine dissolved organic matter from 109 Swedish lakes using ultrahigh-resolution mass spectrometry and optical spectroscopy to investigate the constraints on its persistence in the environment. We find that degradation processes preferentially remove oxidized, aromatic compounds, whereas reduced, aliphatic and N-containing compounds are either resistant to degradation or tightly cycled and thus persist in aquatic systems. The patterns we observe for individual molecules are consistent with our …