The seasonal pattern of microplastics (MPs) contamination of the French littoral area of the Pertuis Charentais, one of the main French shellfish production regions, was assessed for the first time, between May 2019 and May 2020 at four different sites. The reference site was located at “Ile de Ré” and the other sites were located in the estuaries of the Sèvre Niortaise, Charente and Seudre rivers. Both blue mussels (Mytilus edulis) and Pacific oysters (Magallana gigas), that are considered sentinel species for the quality of the marine environment were analysed, along with sediment and seawater samples. MPs were extracted from each sample, counted, measured and sorted by colour and type. Micro-Raman spectroscopy was used to determine the proportion of confirmed MPs and the polymer types. The results showed that the contamination of mussels by fibres and fragments (1.9 ± 2.1 MPs/g ww) was significantly higher than for oysters (0.4 ± 0.4 MPs/g ww). Specifically, the contamination by fibres in both species was significantly greater than the contamination by fragments. Significant variations of MPs contamination were observed across the seasons and sites in bivalves, and depended on the species and the type of MPs (fibres or fragments). Mean concentrations of MPs measured in water and sediment were 0.007 MPs/L and 210 MPs/kg dw, respectively. Finally, blue was the dominant colour for fibres (79%) and fragments (81%). Blue fragments were mainly made of PS (70%) followed by PC (18%) and PP, PA or PLA (3%) whereas blue fibres were mainly made of PA (80%) followed by PET (13%) or PP (7%). This rare environmental case study of long-term chronic exposure of farming areas to MPs provides new knowledge on in situ variations of plastic fibres and fragments contamination throughout the seasons.