The case study presented in the paper is the first in the field to find microplastic (MP) particles in both grey water (GW) and post-treatment sewage (TS) samples, which can also be legally discharged into specially protected areas. Compiling a data set of 50 water samples collected from the GW and TS samples of 5 transport ships involved in the case study, we show that the mean number of separated microparticles in the GW samples n = 72 particles per litre, and in the TS samples n = 51 particles per litre. Of the 614 separated particles, the most common were fibres n = 285 (46.4%), followed by other (various) hard particles n = 226 (36.8%) and soft particles n = 104 (16.8%). Attenuated total reflectance Fourier transform infrared spectroscopy (ATR FT-IR) identification was mainly in the form polyethylene (PE), polypropylene (PP) (solid particles and films), polyesters, polyamides, and acrylic fibres. Scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS) analysis revealed ecotoxic chemical elements on the surface of these particles. Our results show that the sewage treatment facilities installed on ships need to be improved, and we developed a solution for this. The findings of the case study certainly deserve further attention and serve as an impetus for research on the improvement of ship wastewater treatment facilities.