Oysters modify the planktonic microbial community structure by their filtration and NH4 excretion activities. While many studies have been conducted on this subject with adult oysters, none had been carried out in situ with juveniles. Pacific oyster juveniles (Magallana gigas, previously Crassostrea gigas) died massively all over the world since 2008 in relation with OsHV-1 infection. During mortality episodes, sick and dead oysters are not separated from healthy live ones, and left to decay in the surrounding environment, with unknown consequences for the nutrient cycle and planktonic microbial components (PMC). The present study aimed to elucidate for the first time the interactions between oyster juveniles and PMC during a mortality episode. Innovative 425-L pelagic chambers were deployed weekly in situ around oyster lanterns along a stocking-density gradient in the Thau Mediterranean lagoon (France) before, during and after an oyster mortality episode, from April to May 2015. This study reveals (i) significant changes of planktonic microbial community structure during mortality episodes, with a proliferation of picoplankton (<3 μm) and ciliates (Balanion sp., Uronema sp.) within 2 weeks when mortality rates and numbers of moribund juvenile oysters were highest. These changes were probably induced by oyster tissue leaching, decomposition and mineralization, which probably began during the moribund period, as suggested by an increase of PO4 concentration and N:P ratio decrease, (ii) oyster juveniles mainly retained 3–20 μm plankton. In contrast to adults, picophytoplankton and small heterotrophic flagellates (<3 μm) were significantly depleted in the presence of oyster juveniles. Depletion of picoplankton occurred only at the starting of the mortality episode and during the moribund phase. (iii) Oyster juvenile filtration and mortality shifted the planktonic microbial structure toward a heterotrophic microbial system, where ciliates and heterotrophic flagellates acted as a trophic link between picoplankton and oysters. The next stage of our investigation is to examine the effect of a mortality episode on pathogen fluxes in the water column, exploring their relationships with planktonic components and dead oyster flesh.