Abstract The appearance of submesoscale structures in the Gulf of Finland was investigated using model simulations for series of coastal upwelling events in July–September 2006. We applied the Princeton Ocean Model. The horizontal step of the model grid was refined to 0.5, 0.25 and 0.125 nautical miles in the gulf and reached 4 times the resolution in the rest of the Baltic Sea; there were 60 σ -levels in the vertical direction for all simulations. The contribution of salinity to the strength of baroclinic front of upwelling along the northern and southern coasts and thereby to the submesoscale dynamics of the gulf's surface layer was analyzed. Model results with refinement of the grid size to 0.125 nautical miles revealed different forms of submesoscale structures in the gulf's surface layer such as the high Rossby number (Ro) threads (elongated spots of Ro > 1 with typical width and length of 2–3 km and 10–50 km, respectively), cyclonic vortices with Ro > 1 core of 4–6 km diameter, and spiral cyclonic eddies (spirally wrapped high Rossby number threads) of 10–15 km diameter. The high potential vorticity threads presumably formed during the development phase, while the cyclonic vortices and spiral cyclonic eddies during the relaxation phase of upwelling. One of the simulated submesoscale cyclonic eddies, at the beginning with the Ro > 1 core extension as deep as 31–66 m was traced for the period of 33 days. The power spectral density of temperature and velocity fluctuations in the surface layer pointed at some increase of spectral levels and shallowing of spectral slopes towards − 2 on the shorter (submesoscale) wavelengths with the refinement of model grid.