A high resolution numerical study is undertaken to simulate an upwelling event along the northern coast of the Gulf of Finland, 21–29 July 1999, which was documented well by in situ and remote measurements. The simulated sequence of SST maps shows a reasonably good resemblance to that of satellite infrared imagery, including both mesoscale coherent structures (filaments or squirts) and the whole process of post-upwelling relaxation of the temperature field. Upwelling along the northern coast of the Gulf is accompanied by downwelling along the southern coast so that two longshore baroclinic jets and related fronts are developed simultaneously. When the strong westerly winds producing the upwelling/downwelling weaken, the longshore jets become unstable and produce transverse jets, cold/warm water squirts. Using pseudo-random simulated fields of temperature and velocity of currents, the apparent lateral diffusivity due to squirts is directly estimated at 500 m2 s−1. The model is also applied to estimate nutrient transport. Simulated phosphate concentration in the surface layer at the cold side of upwelling front is found to be about 0.3 mmol m−3 which is consistent with observations. The total content of phosphorus and nitrogen in the upper 10 m layer of the Gulf introduced by the upwelling event is estimated to be 387 and 36 tons, respectively. It follows, that the upwelling event transports nutrients into the upper layer with clear excess of phosphorus (N:P = 36:387 = 0.093) compared to the Redfield ratio of 7.2. Therefore phosphorus input caused by upwelling during summer most likely promotes nitrogen-fixing cyanobacteria blooms.