Fluxes and molecular compositions of a group of major biochemical classes (lipids, lignin, pigments, amino acids, and carbohydrates) were compared among sediment traps treated with different poisons and preservatives and deployed for 1–2 months in a coastal marine environment. Fluxes and compositions of biochemicals were significantly more variable than bulk particle fluxes and elemental compositions. This observation was attributed to a greater influence of dead zooplankton “swimmers” in treated traps rather than differences in microbial decomposition due to the various treatments. Molecular compositions, especially of lipids, confirm the influence of zooplankton swimmers on the biochemical composition of the particulate material in treated traps compared to untreated controls even when large swimmers had been removed. An inventory of the major biochemicals we measured accounted for 25–45% of the organic carbon in our samples, with amino acids and sugars making up the bulk (80–90%) of the identified carbon.