We consider upwelling and downwelling dynamics in an idealized ocean model configuration of the Western Gotland Basin in the Baltic Sea, featuring a gently sloping bottom in the west and a steep bathymetry in the east. Typical transient wind conditions and seasonally variable stratification are examined. Upwelling and downwelling jets develop at the coastal boundaries and interact through cross-shore boundary-layer flows. Initial evolution of the coastal jets is consistent with linear theory. The front position and the onset of instability is governed by the wind forcing, with a weak dependence on seasonal stratification. The unstable growth rates and wavelengths over the slope depend on the relative orientation of the slope and isopycnals, consistent with theory. The upwelling jets become baroclinically unstable during the wind-forced phase, whereas instability onset for downwelling on the slope is after 2–3 weeks (during the relaxation phase). The downwelling on the steep side is consistently stable. The regime with unstable upwelling on the slope side with concurrent stable downwelling on the steep side is more frequent (southwesterly winds: 30% occurrence) and leads to strong cross-shore transport. Unstable downwelling on the slope with upwelling on the steep side is a rarer event (northwesterly winds: 10% occurrence) and generates strong vertical mixing on the slope, with implications for oxygen and nutrient fluxes on the inner shelf along the Swedish coast. Baroclinic eddies contribute to elevated vertical mixing in the surface layer.

Excessive nutrient inputs have caused eutrophication of coastal ecosystems worldwide, triggering extensive algal blooms, oxygen-depletion, and collapse of local fisheries. In the Baltic Sea, inputs of nitrogen (N) and phosphorus (P) have been significantly reduced since the 1980s, but the environmental state shows little to no signs of recovery. However, a simulation with continued high loads from the mid-1980s demonstrates that while the state has not improved yet, it would be considerably worse today without the load reductions (e.g., 82% larger oxygen-free bottom areas and 104% and 58% higher wintertime concentrations of inorganic N and P, respectively, in the Baltic Proper). Additional simulations with current nutrient loads continuing into the future indicate that conditions will likely improve in the coming decades. This study underscores the significance of acting on early warning signs of eutrophication, and furthermore how sustained efforts to decrease nutrient loads can mitigate the severity of eutrophication.

Coastal areas are an important source of methane (CH4). However, the exact origins of CH4 in the surface waters of coastal regions, which in turn drive sea-air emissions, remain uncertain. To gain a comprehensive understanding of the current and future climate change feedbacks, it is crucial to identify these CH4 sources and processes that regulate its formation and oxidation. This study investigated coastal CH4 dynamics by comparing water column data from six stations located in the brackish Tvärminne Archipelago, Baltic Sea. The sediment biogeochemistry and microbiology were further investigated at two stations (i.e., nearshore and offshore). These stations differed in terms of stratification, bottom water redox conditions, and organic matter loading. At the nearshore station, CH4 diffusion from the sediment into the water column was negligible, because nearly all CH4 was oxidized within the upper sediment column before reaching the sediment surface. On the other hand, at the offshore station, there was significant benthic diffusion of CH4, albeit the majority underwent oxidation before reaching the sediment-water interface, due to shoaling of the sulfate methane transition zone (SMTZ). The potential contribution of CH4 production in the water column was evaluated and was found to be negligible. After examining the isotopic signatures of δ13C-CH4 across the sediment and water column, it became apparent that the surface water δ13C-CH4 values observed in areas with thermal stratification could not be explained by diffusion, advective fluxes, nor production in the water column. In fact, these values bore a remarkable resemblance to those detected below the SMTZ. This supports the hypothesis that the source of CH4 in surface waters is more likely to originate from ebullition than diffusion in stratified brackish coastal systems.

The tightening of the removal requirements in the new Urban Wastewater Treatment Directive is unlikely to have a decisive effect on the nutrient inputs, since most wastewater treatment in the total Baltic Sea drainage basin has improved to the proposed requirements in recent decades. The actions on stormwater overflows and urban runoff could, however, be of importance. Further reductions on nutrient inputs from wastewater could be achieved through measures beyond the directive, such as regulations on private sewages in scattered dwellings and mandatory tertiary treatment of both nitrogen and phosphorus in the whole drainage basin.

We have constructed a nutrient fate model for the Baltic Sea that links anthropogenic nitrogen and phosphorus inputs to the catchment to the dynamics of waterborne loads to the Baltic Sea, covering the time-period from 1900 to present. During this period, nutrient inputs to the drainage basin approximately tripled to a peak in the 1980s, after which they declined. Our model accounts for temporary nutrient storage on land and in inland waters, forming active legacy pools that contribute to nutrient export to the Baltic Sea, and for nutrient removal by terrestrial and aquatic sinks. The model indicates that response times to changes in anthropogenic nutrient inputs to the drainage basin are approximately 4 years for riverine nitrogen and 6–18 years for riverine phosphorus loads. Mineral fertilizer use in agriculture dominates nutrient inputs to the drainage basin, whereas the composition of riverine loads also depends on the collection and treatment of domestic sewage. Removal by terrestrial and aquatic nutrient sinks was the dominant fate of both nitrogen and phosphorus in our model. The amount of nutrients currently stored in legacy pools is therefore much smaller than what the difference between cumulative nutrient inputs to the catchment and the export to the sea suggests. Nevertheless, mobilization from these storage pools is the primary contribution to current anthropogenic riverine nutrient loads to the Baltic Sea. For phosphorus, the legacy effects of past reductions in inputs to the catchment can entail a significant, yet unrealized contribution toward the load reductions stipulated by Baltic Sea management plans. Therefore, accounting for nutrient storage, time-lags, and legacy effects could notably reduce the need for additional future mitigation measures.

Methane (CH4) cycling in the Baltic Sea is studied through model simulations that incorporate the stable isotopes of CH4 (12C-CH4 and 13C-CH4) in a physical-biogeochemical model. A major uncertainty is that spatial and temporal variations in the sediment source are not well known. Furthermore, the coarse spatial resolution prevents the model from resolving shallow-water near-shore areas for which measurements indicate occurrences of considerably higher CH4 concentrations and emissions compared with the open Baltic Sea. A preliminary CH4 budget for the central Baltic Sea (the Baltic Proper) identifies benthic release as the dominant CH4 source, which is largely balanced by oxidation in the water column and to a smaller degree by outgassing. The contributions from river loads and lateral exchange with adjacent areas are of marginal importance. Simulated total CH4 emissions from the Baltic Proper correspond to an average ∼1/41.5 mmol CH4 m-2 yr-1, which can be compared to a fitted sediment source of ∼1/418 mmol CH4 m-2 yr-1. A large-scale approach is used in this study, but the parameterizations and parameters presented here could also be implemented in models of near-shore areas where CH4 concentrations and fluxes are typically substantially larger and more variable. Currently, it is not known how important local shallow-water CH4 hotspots are compared with the open water outgassing in the Baltic Sea.

Intensive agriculture has been linked to increased nitrogen loads and adverse effects on downstream aquatic ecosystems. Sustained large net nitrogen surpluses have been shown in several contexts to form legacies in soil or waters, which delay the effects of reduction measures. In this study, detailed land use and agricultural statistics were used to reconstruct the annual nitrogen surpluses in three agriculture-dominated watersheds of Denmark (600-2700 km2) with well-drained loamy soils. These surpluses and long-term hydrological records were used as inputs to the process model ELEMeNT to quantify the nitrogen stores and fluxes for 1920-2020. A multi-objective calibration using timeseries of river nitrate loads, as well as other non-conventional data sources, allowed to explore the potential of these different data to constrain the nitrogen cycling model. We found the flux-weighted nitrate concentrations in the root zone percolate below croplands, a dataset not commonly used in calibrating watershed models, to be critical in reducing parameter uncertainty. Groundwater nitrate legacies built up in all three studied watersheds during 1950-1990 corresponding to & SIM;2% of the surplus (or & SIM;1 kg N ha yr-1) before they went down at a similar rate during 1990-2015. Over the same periods active soil nitrogen legacies first accumulated by approximately 10% of the surplus (& SIM;5 kg N ha yr-1), before undergoing a commensurate reduction. Both legacies appear to have been the drivers of hysteresis in the diffuse load at the catchments' outlet and hindrances to reaching water quality goals. Results indicate that the low cropland surpluses enforced during 2008-2015 had a larger impact on the diffuse river loads than the European Union's untargeted grass set-aside policy of 1993-2008. Collectively, the measures of 1990-2015 are estimated to have reset the diffuse load regimes of the watersheds back to the situation prevailing in the 1960s.

Increasing atmospheric CO₂ drives ocean acidification globally. In coastal seas, acidification trends can however be either counteracted or enhanced by other processes. Ecosystem effects of acidification are so far small in the Baltic Sea, but changes should be anticipated unless CO₂ emissions are curbed. Possible future acidification trends in the Baltic Sea, conditional on CO₂ emissions, climate change, and changes in productivity, can be assessed by means of model simulations. There are uncertainties regarding potential consequences for marine organisms, partly because of difficulties to assign critical thresholds, but also because of knowledge gaps regarding species’ capacity to adapt. Increased temporal and spatial monitoring of inorganic carbon system parameters would allow a better understanding of current acidification trends and also improve the capacity to predict possible future changes. An additional benefit is that such measurements also provide quantitative estimates of productivity. The technology required for precise measurements of the inorganic carbon system is readily available today. Regularly updated status evaluations of acidification, and the inorganic carbon system in general, would support management when assessing climate change effects, eutrophication or characteristics of the pelagic habitats. This would, however, have to be based on a spatially and temporally sufficient monitoring program.

Turbulent diapycnal mixing is important for the estuarine circulation between basins of the Baltic Sea as well as for its local ecosystems, in particular with regard to eutrophication and anoxic conditions. While the interior of the basins is overall relatively calm, stratified flow over steep bathymetric features is known as a source of strong turbulent mixing. Yet, current in situ observations often cannot capture the spatio-temporal development of dynamic and intermittent turbulent mixing related to overflows over rough bathymetry. We present observational oceanographic data together with openly accessible high-resolution bathymetry from a prototypical sill and an adjacent deep channel in the sparsely sampled Southern Quark located in the Åland Sea, connecting the northern Baltic Proper with the Bothnian Sea. Our data were acquired during two 1-week cruises on R/V Electra in February-March 2019 and 2020. We collected high-resolution broadband acoustic observations of turbulent mixing together with in situ microstructure profiler measurements, and current velocities from acoustic Doppler current profilers. We found that a temporally reversing non-tidal stratified flow over the steep bathymetric sill created a dynamic and extremely energetic environment. The observed flow reversed during both cruises on timescales of a few days. Saltier, warmer, and less oxygenated deep water south of the sill was partly blocked, the reversing flow was at times hydraulically controlled with hydraulic jumps occurring on both sides of the sill, and high spatial variability occurred in the surface layer on small scales. Dissipation rates of turbulent kinetic energy, vertical turbulent diffusivities, and vertical salt flux rates were increased by 3-4 orders of magnitude in the entire water column in the vicinity of the sill compared to reference stations not directly influenced by the overflow with average dissipation rates near the sill between 10-7 and 10-6 W kg-1, average vertical diffusivities of 0.001 m2 s-1 in the halocline and up to 0.1 m2 s-1 below the halocline, and average vertical salt flux rates around 0.01 g m-2 s-1 in the halocline and between 0.1 and 1 g m-2 s-1 below the halocline. We suggest, based on acoustic observations and in situ measurements, that the underlying mechanism for the highly increased mixing across the halocline is a combination of shear and topographic lee waves breaking at the halocline interface. We anticipate that the resulting deep- and surface-water modification in the Southern Quark directly impacts exchange processes between the Bothnian Sea and the northern Baltic Proper and that the observed mixing is likely important for oxygen and nutrient conditions in the Bothnian Sea.

Location, specific topography, and hydrographic setting together with climate change and strong anthropogenic pressure are the main factors shaping the biogeochemical functioning and thus also the ecological status of the Baltic Sea. The recent decades have brought significant changes in the Baltic Sea. First, the rising nutrient loads from land in the second half of the 20th century led to eutrophication and spreading of hypoxic and anoxic areas, for which permanent stratification of the water column and limited ventilation of deep-water layers made favourable conditions. Since the 1980s the nutrient loads to the Baltic Sea have been continuously decreasing. This, however, has so far not resulted in significant improvements in oxygen availability in the deep regions, which has revealed a slow response time of the system to the reduction of the land-derived nutrient loads. Responsible for that is the low burial efficiency of phosphorus at anoxic conditions and its remobilization from sediments when conditions change from oxic to anoxic. This results in a stoichiometric excess of phosphorus available for organic-matter production, which promotes the growth of N₂-fixing cyanobacteria and in turn supports eutrophication.

This assessment reviews the available and published knowledge on the biogeochemical functioning of the Baltic Sea. In its content, the paper covers the aspects related to changes in carbon, nitrogen, and phosphorus (C, N, and P) external loads, their transformations in the coastal zone, changes in organic-matter production (eutrophication) and remineralization (oxygen availability), and the role of sediments in burial and turnover of C, N, and P. In addition to that, this paper focuses also on changes in the marine CO₂ system, the structure and functioning of the microbial community, and the role of contaminants for biogeochemical processes. This comprehensive assessment allowed also for identifying knowledge gaps and future research needs in the field of marine biogeochemistry in the Baltic Sea.