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The extent to which sinking particles disaggregate and exchange with surrounding material affects the efficiency of particulate organic carbon export to the deep sea. In 2003 and 2005, we compared the pigment and amino acid compositions of sediment trap and in situ pump samples collected in the northwest Mediterranean Sea to assess exchange between sinking and suspended particles. While sediment traps collected only sinking particles, in situ pumps collected both larger (> 70‐µm) particles, believed to represent the sinking fraction, as well as smaller (1–70‐µm) particles, believed to represent the suspended fraction. The organic compound compositions of sinking and suspended particles were very different and remained consistently so with depth, suggesting that exchange between them was limited. This difference was particularly pronounced during the high flux periods in spring. Sinking particles appeared to be composed of many fecal pellets and a few phytoplankton aggregates, and were enriched in diatom indicators. Suspended particles appeared to be more enriched in fresh phytoplankton and contained indicators of calcium carbonate‐bearing organisms. During the low‐flux summer period, the contribution of fecal pellet indicators to sinking particles was lower, whereas the contribution of microbial degradation products in both particle types was higher, possibly indicating greater exchange during periods of low flux when fecal pellets were not as abundant. Results from this study suggest that fecal pellets, although already degraded upon formation, are more robust than phytoplankton aggregates and, therefore, more likely to resist disaggregation and further decomposition during transit through the water column.

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