Understanding the dynamics of marine dissolved organic carbon (DOC) is essential for predicting its role in carbon cycling and its response to climate change. Here, we unveil molecular transformations of marine chromophoric dissolved organic matter (CDOM) across the global ocean using Ultraviolet-visible spectroscopy. Significant variability in CDOM composition within the epi- and mesopelagic layers ( < 1000 m) correlates with physicochemical parameters, driven by irradiation, primary production, biological activity, transport, and riverine inputs. In the bathypelagic layer (1000–5000 m), up to 18.2% of highly conjugated molecules transform into low-molecular-weight CDOM, despite stable DOC concentrations. This dynamic process sustains biomass production and respiration in deep ocean, contributing a carbon flux of 3–24 Pg C yr−1—up to an order of magnitude more than the fast-sinking particulate organic carbon flux. Our findings offer insights into the molecular transformation of deep-ocean DOM and underscore the need to reassess the bathypelagic DOC pool’s role in the global carbon cycle.
