Dissolved organic matter (DOM) plays a crucial role in global carbon cycling, yet its molecular complexity and the factors governing its turnover and degradation in different ecosystems are poorly understood. Here, we provide an experimental assessment of structural diversity in terrestrial and marine DOM, using a multimethod approach. Terrestrial peat pore water (PPW) exhibited a similar number of COOH-groups, two times more noncarboxylic oxygen atoms (non-COOH-O, up to <i>n</i> = 20) as compared to surface seawater (SSW; up to <i>n</i> = 10), and significantly higher isomeric dispersity indices (2.5-3.0 vs 1.3-1.5), highlighting its greater structural complexity and isomeric diversity. At the level of individual molecular formulas of the widely used DOM degradation index (<i>I</i>_DEG), we found that POS_IDEG molecular formulas representing fresh DOM (i.e., they were positively correlated with radiocarbon content) share similar structural characteristics in both environments (e.g., low number of carboxyl-groups). In contrast, NEG_IDEG markers for degraded DOM (i.e., negatively correlated with radiocarbon content) displayed a higher number of carboxyl-groups in the least acidic fraction for PPW but in the most acidic fraction for SSW. Our results indicate ecosystem-specific degradation pathways emphasizing how global carbon cycling is influenced by the molecular structure of DOM.