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The oligotrophic Adriatic Sea is characterized during a typical summer by low productivity caused by strong water column stratification, which inhibits vertical mixing and nutrient supply to the euphotic zone. These conditions can be disrupted by transient physical forcing, which enhances nutrient fluxes and creates localized hotspots of relatively high net primary production. In this study, plankton abundance and diversity were investigated in relation to the physical forcing and nutrient concentrations in an area affected by island-trapped waves (ITWs) near Lastovo Island (Adriatic Sea). The episodic ITW events resulted in enhanced uplift and vertical excursion of the thermocline, marked by anomalously higher nutrient concentrations and a corresponding increase in net primary production in the thermocline layer. Physicochemical properties explained 11.7 % (p = 0.002) of the variability in micro- and nanophytoplankton and 88.9 % (p = 0.001) in the picoplankton community. A significant response to the ITW phenomenon in the plankton community composition (p = 0.001) was observed for bacterioplankton. Among the identified amplicon sequence variances, primary producers were scarce and mainly represented cyanobacteria (Synechococcus strain CC9902), stramenopiles (Pelagomonas), and chlorophytes (Ostreococcus). The remaining amplicon sequence variances were assigned to the classes Copepoda, parasitic fungi (Meyerozyma spp.), mixotrophic dinoflagellates (family Peridiniales, mostly the genus Blastodinium), and parasitic Ciliophora (Scuticociliata). Bacterial ecological functions corresponded to chemoheterotrophic, degradation, and fermentation processes, whereas samples collected after the most intense ITW episode also showed abundant bacteria linked to microplastic degradation and parasitosis. These results highlight the ecological role of localized physical phenomena in enhancing nearshore primary productivity and fine shifts in plankton taxa in oligotrophic systems.