Microplastics (MPs) pollution is one of the most important problems of the Earth. They have been found in all the natural environments, including oceans and the atmosphere. In this study, the concentrations of both atmospheric and marine MPs were measured over the Baltic along a research cruise that started in the Gdansk harbour, till the Gotland island, and the way back. A deposition box (based on a combination of active/passive sampling) was used to collect airborne MPs while, marine MPs concentrations were investigated during the cruise using a dedicated net. Ancillary data were obtained using a combination of particle counters (OPC, LAS and CPC), Aethalometer (AE33 Magee Scientific), spectrofluorometer (sea surface samples, Varian Cary Eclipse), and meteorological sensors. Results showed airborne microplastics average concentrations higher in the Gdansk harbour (161 ± 75 m−3) compared to the open Baltic Sea and to the Gotland island (24 ± 9 and 45 ± 20 m−3). These latter values are closer to the ones measured in the sea (79 ± 18 m−3). The MPs composition was investigated using μ-Raman (for the airborne ones) and FTIR (for marine ones); similar results (e.g. polyethylene, polyethylene terephthalates, polyurethane) were found in the two environmental compartments. The concentrations and similar composition in air and sea suggested a linkage between the two compartments. For this purpose, the atmospheric MPs' equivalent aerodynamic diameter was calculated (28 ± 3 μm) first showing the capability of atmospheric MPs to remain suspended in the air. At the same time, the computed turnover times (0.3–90 h; depending on MPs size) limited the transport distance range. The estimated MPs sea emission fluxes (4–18 ∗ 106 μm3 m−2 s−1 range) finally showed the contemporary presence of atmospheric transport together with a continuous emission from the sea surface enabling a grasshopper long-range transport of microplastics across the sea. Display omitted •Airborne and marine microplastics were sampled during a cruise over the Baltic.•The concentration, shape, colour, size, and type of microplastics were recorded.•Microplastic fluxes and turnover times were calculated.•An interplay of atmospheric transport together with emissions from the sea was seen.•Microplastics deposited to the sea could be re-emitted many times.