Marine phytoplankton is a key component of natural capital, supporting ecosystem functioning and the provision of ecosystem services related to seafood production. Harmful algal blooms (HABs) can impact these services by producing biotoxins that accumulate along the food chain, in particular in shellfish Mytilus galloprovincialis tissues. Within the PNRR PRIN ENDRIMUS Project, temporal and spatial variability of phytoplankton communities was investigated, with emphasis on potentially toxic taxa, and their influence on physiological and skeletal traits of mussels along the Adriatic coast. Significant spatial and seasonal differences were observed in chlorophyll-a (Chl-a), particulate matter and phytoplankton. Chl-a concentrations were found to be elevated during winter and spring months. Particulate organic matter peaked in spring, particulate inorganic matter in autumn and total phytoplankton abundances in winter. Meanwhile, qPCR analyses revealed marked variability in target diatom and dinoflagellate taxa in mussel tissues. qPCR approach revealed consistent trophic exposure of mussels to dominant diatoms such as Chaetoceros socialis, with the highest accumulation during winter. Dinoflagellates were consistently detected in mussel tissues. Notably, toxic dinoflagellate Dinophysis spp., occurring at low concentrations in water column, was positively detected in mussel tissues (up to 10² cells g⁻¹), with peaks in winter and spring, indicating persistent exposure to potentially toxic taxon even in the absence of bloom conditions. Furthermore, the random forest analyses indicated that shell properties responded primarily to particulate matter, salinity, and carbonate chemistry, while trophic variables, including dinoflagellates, small phytoplankton fractions, and toxic Dinophysis spp. in tissues, emerged as key predictors of condition index (CI), accounting for 36.8% of its variance. These findings demonstrated that plankton biodiversity, including low-abundance harmful taxa, influences shellfish condition and should be considered in ecosystem-based aquaculture management. The detection of Dinophysis spp. in mussel tissues highlights the importance of monitoring harmful algal taxa even in the absence of bloom conditions.