We review progress in Baltic Sea physical oceanography (including sea ice and atmosphere-land interactions) and Baltic Sea modelling, focusing on research related to BALTEX Phase II and other relevant work during the 2003-2014 period. The major advances achieved in this period are: Meteorological databases are now available to the research community, partly as station data, with a growing number of freely available gridded datasets on decadal and centennial time scales. The free availability of meteorological datasets supports the development of more accurate forcing functions for Baltic Sea models. In the last decade, oceanographic data have become much more accessible and new important measurement platforms, such as FerryBoxes and satellites, have provided better temporally and spatially resolved observations. Our understanding of how large-scale atmospheric circulation affects the Baltic Sea climate, particularly in winter, has improved. Internal variability is strong illustrating the dominant stochastic behaviour of the atmosphere. The heat and water cycles of the Baltic Sea are better understood. The importance of surface waves in air-sea interaction is better understood, and Stokes drift and Langmuir circulation have been identified as likely playing an important role in surface water mixing in sea water. We better understand sea ice dynamics and thermodynamics in the coastal zone where sea ice interaction between land and sea is crucial. The Baltic Sea's various straits and sills are of increasing interest in seeking to understand water exchange and mixing. There has been increased research into the Baltic Sea coastal zone, particularly into upwelling, in the past decade. Modelling of the Baltic Sea-North Sea system, including the development of coupled land-sea-atmosphere models, has improved. Despite marked progress in Baltic Sea research over the last decade, several gaps remain in our knowledge and understanding. The current understanding of salinity changes is limited, and future projections of salinity evolution are uncertain. In addition, modelling of the hydrological cycle in atmospheric climate models is severely biased. More detailed investigations of regional precipitation and evaporation patterns (including runoff), atmospheric variability, highly saline water inflows, exchange between sub-basins, circulation, and especially turbulent mixing are still needed. Furthermore, more highly resolved oceanographic models are necessary. In addition, models that incorporate more advanced carbon cycle and ecosystem descriptions and improved description of water-sediment interactions are needed. There is also a need for new climate projections and simulations with improved atmospheric and oceanographic coupled model systems. These and other research challenges are addressed by the recently formed Baltic Earth research programme, the successor of the BALTEX programme, which ended in 2013. Baltic Earth will treat anthropogenic changes and impacts together with their natural drivers. Baltic Earth will serve as a network for earth system sciences in the region, following in the BALTEX tradition but in a wider context.

Salinity and halocline depth variations in the Baltic Sea during 1961–2007 are studied using a three‐dimensional ocean circulation model. Significant interannual and interdecadal variations in the halocline depth are found, together with distinct periods characterized either by shallow (1970–1975) or deep halocline (1990–1995). The model simulation indicates that the mean top layer salinity in the Baltic Sea is mainly controlled by the accumulated river runoff, while the mean below halocline salinity in the Baltic proper (which comprises Bornholm and Gotland basins) is more dependent on the low‐pass filtered zonal wind stress, with cutoff period of 4 years, henceforth called the mean zonal wind stress. The halocline depth and stratification strength in the Baltic Sea are significantly affected by the mean zonal wind stress, while the impact of runoff is smaller. The ventilation of the halocline from bottom layers is stronger during the shallow and from surface layers during the deep halocline period. Due to changes in ventilation variations in halocline depth systematically affect bottom oxygen concentrations on seasonal and decadal, but not on interannual time scales. For instance, a deeper halocline reduces hypoxic (oxygen concentration in bottom water below 2 mL/L) and anoxic (anoxic conditions in bottom water) areas and increases the bottom oxygen concentrations in the Gulf of Finland but decreases them in the deeper parts of the Baltic proper. Model results suggest that due to undersampling during 1961–2007 mean hypoxic and anoxic areas calculated from observed profiles are underestimated by 41% and 43%, respectively.

The reversal of estuarine circulation caused by southwesterly wind forcing may lead to vanishing of stratification and subsequently to oxygenation of deep layers during the winter in the Gulf of Finland. Six conductivity, temperature, depth (CTD)+oxygen transects (130 km long, 10 stations) were conducted along the thalweg from the western boundary to the central gulf (21 December 2011–8 May 2012). Two bottom-mounted ADCP were installed, one near the western border and the second in the central gulf. A CTD with a dissolved oxygen sensor was deployed close to the western ADCP. Periods of typical estuarine circulation were characterized by strong stratification, high salinity, hypoxic conditions and inflow to the gulf in the near-bottom layer. Two circulation reversals were observed: one in December–January and one in February. The first reversal event was well developed; it caused the disappearance of the stratification and an increase in the oxygen concentration from hypoxic values to 270 μmol L⁻¹ (to 6 mL L⁻¹) throughout the water column along the thalweg and lasted approximately 1.5 months. Shifts from estuarine circulation to reversed circulation and vice versa were both associated with strong longitudinal (east–west) gulf currents (up to 40 cm s⁻¹) in the deep layer. The change from oxygenated to hypoxic conditions in the western near-entrance area of the gulf occurred very rapidly, within less than a day, due to the intrusion of the hypoxic salt wedge from the NE Baltic Proper. In the eastern part of the gulf, good oxygen conditions caused by reversals remained for a few months.