Phytoplankton size is a significant functional trait affecting many ecological processes and influencing the carbon fate and the trophic regimes of the ecosystems. In this study, we examined the effect of the lateral advection of nutrient-rich Messina Mixed Waters on the phytoplankton size structure and community composition in the euphotic layer of the Gulf of Augusta (Western Ionian Sea) in early autumn. The chlorophyll a concentration ranged from 0.08 to 0.8 mg m−3 and the phytoplankton abundances ranged from 21 × 103 to 245 × 103 cells L−1. The size structure of phytoplankton biomass, obtained by sequential filtration of water samples, suggested the dominance of micro-planktonic diatoms in an active Deep Chlorophyll Maximum (DCM) whereas smaller forms were mainly represented by phytoflagellates. A short-term tidal-induced variability of the assemblage structure was observed at a “sentinel” station located at the Gulf shelf-break where lateral advection due to meso-scale dynamics sustained most of the phytoplankton biomass. Our research shows that, in stratified conditions, nutrient enrichment by lateral advection at DCM modifies the size-structure of phytoplankton with respect to that expected from the reference baseline oceanic model validated in open ocean waters. In particular, while smaller fraction incidences reveal a surface oligotrophic system, an increase of the micro-sized fraction is triggered at DCM: this indicates the prevalence of “new production” processes which is a quite unusual condition for the Mediterranean DCM in early autumn, when trophic web is typically sustained by “regenerate production”. Our observations suggest that both “microbial” and “herbivore” pathways could coexist and regulate the carbon flow in the Gulf in this season. •Lateral advection of nutrient-rich waters shaped local phytoplankton size-structure.•Micro-phytoplankton fraction incidence overcomes the reference baseline oceanic model.•A micro-sized diatoms core pool dominated spatial and time-series coastal assemblages.•Meso-scale dynamics influenced phytoplankton composition and relative size incidences.