Abstract With almost 700 Pg of carbon, marine dissolved organic carbon (DOC) stores more carbon than all living biomass on Earth combined. However, the controls behind the persistence and the spatial patterns of DOC concentrations on the basin scale remain largely unknown, precluding quantitative assessments of the fate of this large carbon pool in a changing climate. Net removal rates of DOC along the overturning circulation suggest lifetimes of millennia. These net removal rates are in stark contrast to the turnover times of days to weeks of heterotrophic microorganisms, which are the main consumers of organic carbon in the ocean. Here, we present a dynamic “MICrobial DOC” model (MICDOC) with an explicit representation of picoheterotrophs to test whether ecological mechanisms may lead to observed decadal to millennial net removal rates. MICDOC is in line with >40,000 DOC observations. Contrary to other global models, the reactivity of DOC fractions is not prescribed, but emerges from a dynamic feedback between microbes and DOC governed by carbon and macronutrient availability. A colimitation of macronutrients and organic carbon on microbial DOC uptake explains >70% of the global variation of DOC concentrations, and governs characteristic features of its distribution. Here, decadal to millennial net removal rates emerge from microbial processes acting on time scales of days to weeks, suggesting that the temporal variability of the marine DOC inventory may be larger than previously thought. With MICDOC, we provide a foundation for assessing global effects on DOC related to changes in heterotrophic microbial communities in a future ocean. Plain Language Summary The ocean stores more carbon as dissolved organic compounds (DOC) than all animals and plants on land and the oceans combined. However, numerical models used for future climate scenarios lack an implementation of processes transforming DOC back to CO 2 by marine microorganisms. Here, we present a global dynamical ocean model that explicitly considers the processes of DOC degradation by marine microorganisms. In the present ocean, the availability of organic carbon but also nitrogen and phosphorus control the amount of carbon stored as DOC, as the lack of these nutrients inhibits its degradation by bacteria. The identification of these ecological controls allows a quantitative assessment of the fate of this large carbon reservoir in the future. The findings indicate that the marine DOC reservoir is potentially more dynamic than previously thought, since decadal to millennial scale net removal rates might be a result of microbial processes acting on shorter time scales. Key Points A model to reconcile millennial‐scale bulk dissolved organic carbon degradation rates and short‐term microbial turnover times is presented Macronutrient colimitation can explain observed concentration patterns of dissolved organic carbon in the surface ocean Continuous microbial reworking suggests a higher temporal variability of the marine dissolved organic matter inventory than previously thought