In the last decade, plastic waste has become one of the main threats to marine ecosystems and their biodiversity due to its abundance and increased persistence. Microplastics can be classified as either primary, i.e., fabricated for commercial use, or secondary, i.e., resulting from the fragmentation/weathering processes of larger plastic pieces in the environment. In general, microplastics are detected in a number of aquatic organisms (e.g., fish, bivalves, mollusks, etc.) with alarming effects on their health. Therefore, the present work focuses on the detection and identification of microplastics in fish species (Dicentrarchus labrax, Sparus aurata) and mussels (Mytilus galloprovincialis) from aquaculture systems since these aquatic organisms are largely commercially available for consumption. In addition, seawater was also screened for the types of polymers present as well as their aging. The experimental protocol for biota samples contains a digestion step using Fenton’s reagent (0.05 M FeSO4⋅7H2O with 30% H2O2 at a volume ratio of 1:1) to remove organic material followed by filtration and a density separation step where the sample material was mixed with a saturated ZnCl2 solution to separate microplastic particles from heavier material. For seawater samples (sampled by a microplastic net sampler), only sieving on stainless steel sieves followed by filtration on silica filters was applied. Detection of microplastics and identification of their polymeric composition was achieved through the combined use of micro-Raman analysis, Attenuated Total Reflectance–Fourier Transform Infrared spectroscopy, and Scanning Electron Microscopy in tandem with Energy Dispersive X-ray spectroscopy. Microplastic abundance was 16 ± 1.7 items/individual in mussels and 22 ± 2.1 items/individual in sea bass, and 40 ± 3.9 items/individual in sea bream, with polyethylene (74.4%) being the most detected polymer type, while polyethylene-co-vinyl acetate (65%), polyvinyl-butyral (36.8%), polyvinyl alcohol (20%), and polybutyl methacrylate (15.8%) were also detected to a lesser extent. The microplastics isolated from seawater samples were films (30%), fragments (30%), and fibers (20%), while some of them were derived from foams (20%). Also, in most of these seawater-recovered microplastics, a relatively high degree of oxidation (carbonyl index > 0.31) was observed, which was further confirmed by the results of Energy Dispersive X-ray spectroscopy. Finally, the Scanning Electron Microscopy images showed various morphological characteristics (cracks, cavities, and burrs) on the surfaces of the microplastics, which were attributed to environmental exposure.