The European Union's Marine Strategy Framework Directive (MSFD) aims to assess a “Good Environmental Status” (GES) based on the analysis of 11 Descriptors. Among them, investigating the food webs (Descriptor 4) helps to evaluate the impact of anthropogenic and climate change on the functioning of marine ecosystems. The present study analyzed, with specific ecological indicators, , how environmental conditions (e.g., river inputs) can affect the structure and functionality of planktonic food-webs. An ecological-network modeling approach (based on Ecopath) was conducted along the coast of the Campania Region (central Tyrrhenian Sea, NW Mediterranean) in the three main gulfs (Gaeta, Naples, and Salerno), during two seasonal snapshots (autumn 2020 and summer 2021). The results revealed clear seasonal structural diversity of the planktonic food web, with autumn 2020 showing less network organization, especially in Gaeta, than summer 2021. Specifically, in autumn, Gaeta's microbial food web was primarily dominated by detritivores (e.g., doliolids, appendicularians and salps), whereas in summer, it was centered around primary production and herbivorous processes. Integrating the analysis from satellite data, it was possible to attribute this autumn trophic condition to increased inputs of organic matter of terrestrial origin, transported by the main rivers present in the Gulf of Gaeta. The proposed approach is designed as a tool to inform marine policies and coastal planning, supporting the role of planktonic food-webs in highlighting those coastal marine sectors whose ecosystems are more vulnerable to anthropogenic and natural disturbances.