This study investigates the efficacy of using acid, alkaline, and enzymatic digestion techniques to isolate microplastics from biota-rich seawater samples and marine organisms. The optimized enzymatic protocol can digest over 97% of the material in plankton-rich seawater samples without damaging microplastic debris. The method was applied to replicate marine samples from the western English Channel, identifying 0.27 microplastics per cubic meter. The protocol was also used to extract microplastics ingested by marine zooplankton under laboratory conditions. The findings demonstrate that enzymatic digestion can effectively aid in the detection of microplastic debris within seawater samples and marine biota. The study highlights the importance of developing standardized protocols for monitoring microplastic pollution in various marine habitats, particularly in biologically rich coastal systems.This study investigates the efficacy of using acid, alkaline, and enzymatic digestion techniques to isolate microplastics from biota-rich seawater samples and marine organisms. The optimized enzymatic protocol can digest over 97% of the material in plankton-rich seawater samples without damaging microplastic debris. The method was applied to replicate marine samples from the western English Channel, identifying 0.27 microplastics per cubic meter. The protocol was also used to extract microplastics ingested by marine zooplankton under laboratory conditions. The findings demonstrate that enzymatic digestion can effectively aid in the detection of microplastic debris within seawater samples and marine biota. The study highlights the importance of developing standardized protocols for monitoring microplastic pollution in various marine habitats, particularly in biologically rich coastal systems.