Abstract. Significant research has been carried out in the last decade to describe the CO2 system dynamics in the Baltic Sea. However, there is a lack of knowledge in this field in the NE Baltic Sea, which is the main focus of the present study. We analysed the physical forcing and hydrographic background in the study year (2018) and tried to elucidate the observed patterns of surface water CO2 partial pressure (pCO2) and methane concentrations (cCH4). Surface water pCO2 and cCH4 were continuously measured during six monitoring cruises onboard R/V Salme, covering the Northern Baltic Proper (NBP), the Gulf of Finland (GoF), and the Gulf of Riga (GoR) and all seasons in 2018. The general seasonal pCO2 pattern showed oversaturation in autumn–winter (average relative CO2 saturation 1.2) and undersaturation in spring–summer (average relative CO2 saturation 0.5), but it locally reached the saturation level during the cruises in April, May, and August in the GoR and in August in the GoF. The cCH4 was oversaturated during the entire study period, and the seasonal course was not well exposed on the background of high variability. Surface water pCO2 and cCH4 distributions showed larger spatial variability in the GoR and GoF than in the NBP for all six cruises. We linked the observed local maxima to river bulges, coastal upwelling events, fronts, and occasions when vertical mixing reached the seabed in shallow areas. Seasonal averaging over the CO2 flux suggests a weak sink for atmospheric CO2 for all basins, but high variability and the long periods between cruises (temporal gaps in observation) preclude a clear statement.