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Post‐settlement dispersal is a key process in the recruitment of bivalves. To assess the role of such secondary migrations and to identify potential associated triggers, we conducted an in situ sampling survey during the summer recruitment period on the bivalve assemblages of a coarse‐sediment temperate tidal habitat in the Chausey archipelago (Normandy, France). The dynamics of drifters were studied using three types of settler traps (for example, bedload, pelagic, and sinking transports), and we monitored both the abiotic (hydrological and hydrodynamic conditions) and the trophic (nano‐ and pico‐sized particulate organic matter [POM]; fatty acid composition of POM and sediment organic matter [SOM]) environmental parameters. Such an approach allows the discrimination of passive migration (due to sediment erosion by tidal currents and waves) from active migration (related to recruit behavior). Secondary migrations were observed in 25 bivalve taxa, and these mainly involved decreasing abundances of Mytilidae, Nuculidae, Semelidae, Mactridae, and Lucinidae individuals on the study site, highlighting the crucial role of these processes in highly dynamic coastal benthic assemblages. Surprisingly, the intense post‐settlement dispersal observed at the end of the recruitment season was not synchronized with periods of high hydrodynamic stress but to a change in the structure of phytoplanktonic assemblages, particularly the nanoeukaryotic component. Such a response by bivalve recruits to a trophic pelagic cue—triggering secondary migrations—could result from an increased demand for energy required for active migratory behavior.