The production and transformation of marine chromophoric dissolved organic matter (CDOM) provides a window into the marine biological pump as it is present at all depths and can be measured both in the field and via satellite. However, outside of lignin for terrestrial DOM, few studies have linked marine CDOM characteristics with biomarker indices. In this study, we quantified five fluorescent components of marine CDOM and base-extractable particulate organic matter (BEPOM) in a growth and degradation experiment using a natural plankton assemblage, and compared those results to bacterial abundances, hydrolytic enzyme activities, and amino acid concentrations and associated diagenetic indices. Rotating glass bottles containing plankton were sampled initially (day 0), during the mid-exponential (day 13) and stationary (day 20) growth phases, and again following a dark degradation period that lasted 42 days. Protein-like fluorescence (tryptophan-like and tyrosine-like) was correlated with the total amino acid concentrations for both the DOM and BEPOM through all phases of the incubation. However, tryptophan-like fluorescence showed a stronger correlation for aromatic amino acids. The concentration of particulate organic carbon changed significantly during each phase of the experiment and this substrate correlated with hydrolytic enzyme activities and bacterial abundance. This heterotrophy diagenetically altered the POM during the stationary phase and ultimately resulted in the increased production of more humic-like CDOM after degradation in the dark. Results from this study indicate that CDOM formation and cycling may play a prominent role in the ocean's nitrogen cycle.