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Abstract Particulate organic matter supports pelagic food webs, and the activity of these food webs attenuates the flux of carbon into the ocean interior. Understanding the extent to which microbial and metazoan heterotrophs influence particle dynamics is essential to describing the biological carbon pump and nutrient delivery to deep ecosystems. We present results of bulk and compound‐specific nitrogen stable isotope analyses and a Bayesian mixing model of zooplankton fecal pellets (FP), phytoplankton, and microbial detritus end‐members on size‐fractionated particulate organic matter from 10 depths in the upper 500 m of Monterey Bay, CA. Our results suggest three distinct zones of plankton‐particle interactions in Monterey Bay: primary production and grazing from 0 to 60 m, intense microbial reworking from 60 to 200 m, and inclusion into metazoan food webs below 200 m. Zooplankton FP signatures were found in a <20 μm particle size fraction, both at the approximate depth to which zooplankton migrate at night (∼25–60 m) and in the mesopelagic at the approximate depth to which zooplankton migrate during the day (∼200 m). This finding indicates that fecal pellets were rapidly disaggregated at the depth at which they were produced, which has implications for estimates of zooplankton FP contribution to carbon export and modeling efforts. In some water columns, much of zooplankton FP production may be disaggregated and entrained in the epipelagic zone, above the export depth.