As the plastic production has been rising since the last five decades, so does the concern for the occurrence of microplastic particles (< 5 mm) in the marine environment during the past years. But still by now the extent of this microplastic pollution of coastal waters and the open ocean remains unclear. Since monitoring the abundance of microplastics in the marine environment is requested by the Marine Strategy Framework Directive (MSFD) standardized and reliable methods for the detection of microplastics are urgently needed. Studies differ mainly in their purification methods, aiming to reduce biogenic material in environmental samples without altering the plastic polymers to facilitate a clear assignment of the microplastics. In the present and ongoing study the purification method consists of a treatment with technical enzymes and detergents to reduce the use of oxidants and avoid the use of strong acids as well as the subsequent identification and quantification of microplastics applying Focal Plane Array (FPA)-based µ-Fourier-Transform Infrared (µFT-IR) spectroscopy. A new approach involving the FlowCam (Fluid Imaging Technologies) was used to validate the efficacy of the applied digestion protocol. Hereby untreated plankton samples were run through the FlowCam and compared to the samples after treatment with the various technical enzymes (protease, cellulase and chitinase), sodium dodecyl sulfate and hydrogen peroxide according to protocol regarding changes to particle count, particle sizes and appearance. Furthermore a metabolic fingerprint of every digestion step was drawn up applying the same µFT-IR spectroscopic analysis used for the identification of microplastics. Exemplary results derived by applying the validated protocol show the occurrence of microplastics in sediments of the German coastal waters and highlight the need for a further assessment of the microplastic pollution in various compartments i.e. sediments and surface waters and investigating the link between these two.