The estuarine exchange flow is inherently linked to salt mixing which transports water across isohaline surfaces. For the partially mixed, northwest German Elbe estuary, such mixing occurs predominantly at the channel-shoal transition. Here, we aim to identify the mechanisms leading to such near-shoal mixing. To this end, a highly resolved numerical simulation of the Elbe estuary was accounted for in a process-oriented model performance evaluation and then applied for a selected spring-neap cycle, assessing elevated mixing in space and time. Throughout the spring-neap cycle, the timing of mixing was limited by the availability of stratification rather than tidal energy, leading to an early mixing peak at neap. For the corresponding tidal cycle of most intense mixing, we find two main mechanisms of near-shoal mixing despite a high, topography-related spatial variability: First, lateral straining during flood leads to the formation of a salty bottom layer above flat shoals. This layer can be reinstated during ebb via longitudinal straining. Strong shear leads to intense mixing at the halocline during flood and ebb. Second, the intersection of a sufficiently strong halocline with the turbulent channel sidewalls results in intense boundary layer mixing. Under strong stratification, the intensity of near-shoal mixing relative to channel mixing increases as persistent stratification stabilizes the channel throughout the entire tidal cycle while sidewall mixing intensifies.

Ocean alkalinity enhancement (OAE) has become the focus of intensive research as a potential method for future carbon dioxide removal (CDR). In the Baltic Sea, the deposition of alkaline minerals on the seafloor is one of the considered options, as their dissolution raises local alkalinity. Once the additional alkalinity reaches the sea surface, it increases the ocean’s potential for uptake of atmospheric CO2. A reliable estimation of the vertical transport of dissolved constituents is therefore essential for a model’s applicability to ocean alkalinisation research. While concentrations of seawater ingredients are often straightforward to measure, the corresponding transports of these ingredients by advection and turbulent diffusion are not. Based on an example from the study of ocean alkalinity enhancement, we demonstrate that these transport estimates can exhibit a considerable range of uncertainty even when well-calibrated models are employed. To evaluate the reliability of such estimates by current physical ocean models, we recreated a passive tracer release experiment in the Gotland Deep (Baltic Sea) in three model setups: two hydrodynamic models with differing vertical coordinate systems, including two resolutions for one of the models. The resulting simulations produced substantially different estimates of vertical tracer transport. In the case of OAE, this could lead to considerable variability in the predicted time lags between mineral deposition and sea surface contact and thereby in the desired CO2 drawdown. We conclude that, in addition to typical comparisons with salt and temperature observations, a specific validation of transport processes as a prestudy is necessary to assess whether a hydrodynamic model setup is suitable for research questions that require reliable physical transport estimates. These research questions encompass a range of typical applications of hydrodynamic modelling, including simulating the transport of nutrients, toxic substances, or fish larvae.

Coastal shallow water areas are important carbon dioxide sinks, but their sink strength is significantly reduced by the simultaneous emission of other greenhouse gases such as methane (CH4). These areas are often characterized by strong anthropogenic pressure from adjacent agricultural land use, which leads to increased nutrient input, high biological production, oxygen consumption through remineralization of the organic material produced, and ultimately to increased greenhouse gas production. Despite their outstanding importance for marine greenhouse gas emissions, these areas have been little studied to date and the drivers of the spatial and temporal variability of greenhouse gas distribution are poorly understood. To address this problem, we study a lagoon on the German Baltic Sea coast (Darß-Zingst Bodden chain) using a multidisciplinary approach that combines gas chemical and observational oceanographic methods with modeling. Our investigations in the summer of 2024 and 2025 show that the spatial and temporal variability of CH4 concentration in the water and emissions into the atmosphere are primarily caused by wind-driven oceanographic processes, such as water mass transport and mixing. Notably high CH4 concentrations were recorded primarily in protected reed belts and adjacent drainage ditches, indicating the particular importance of these areas as CH4 sources. The high-frequency measurements of CH4 concentrations (Equilibrator-CRDS) provided evidence that changes in water level and the associated pressure change on the sediment have an impact on the CH4 concentration in the water column. Measurements at the water surface with a floating chamber and an eddy covariance flux tower have shown that gas bubble fluxes play a significant role in atmospheric CH4 fluxes and that the intensity of gas bubble release is influenced by water level fluctuations. Our study thus provides a rare CH4 data set from shallow water areas of the German coast and, through its high-frequency data acquisition, reveals the highly dynamic variability of CH4 concentration development and underscores the importance of oceanographic processes in this context.

The main aim of this work is to provide a comprehensive literature review of the current state of knowledge on submesoscale (SMS) dynamics in the Baltic Sea, with potential implications for other similar coastal and marginal seas. Relevant spatial and temporal scales in the Baltic Sea, as well as idealized quantitative descriptions of SMS instabilities, are presented. The methods for studying SMS processes are described, and the availability of the required research infrastructure and relevant data is discussed. The knowledge on SMS processes and their role in coastal-offshore exchanges, vertical and horizontal mixing, and the development of stratification in the Baltic Sea is reviewed and compared with studies in other regions. Processes at adjacent scales and their links to SMS dynamics, including mesoscale features such as upwelling events, fronts, and baroclinic currents in geostrophic balance, as well as small-scale turbulence, are described. This analysis demonstrates that SMS processes may substantially influence large-scale dynamics of the Baltic Sea, challenging the classical understanding of energy transfer across spatial scales that omits instabilities and feedback loops in the SMS range. The review suggests that SMS processes play a role in the biogeochemical functioning of the Baltic Sea by providing vertical fluxes of substances and redistributing plankton biomass. We emphasize that extensive model validation with high-resolution in-situ data remains an urgent task, and a more accurate description of SMS processes in sub-grid parameterizations within large-scale models is necessary. Gaps in knowledge of SMS dynamics and potential further steps to address them are highlighted

Eutrophication of the Baltic Sea was recognized more than half a century ago, but it remains a major threat to the sea's ecosystem. Requirements developed by the Baltic Marine Environment Protection Commission (formed in 1974) and subsequently implemented in national and European Union law have led to reductions of phosphorus river load by approximately 50% and nitrogen river load by approximately 30% since the 1980s, but so far, the measures have failed to significantly improve the surface water quality. A decades-long accumulation of phosphate and oxygen-sapping substances appeared to reduce the efficiency of the lateral supply of oxygen from intrusions and major Baltic inflows via the narrow Baltic Straits. The dynamic change of, in particular, phosphate cycling in deep waters during these inflows contrasts with the sluggish response to river load reduction measures. Seasonal phosphate recycling in surface water results mainly from exchange with the large deep-water phosphate pool, and this key exchange can be better interpreted based on an improved understanding of its physical drivers.

Anoxia in the central Baltic Sea is caused by the disproportion of the oxygen demand below the Baltic Sea halocline and the capability to transport sufficient amounts of oxygen from the well oxygenated upper water column through the halocline into the deeper Baltic Sea. Despite the fact of anoxia below the halocline, there is a growing evidence for a considerable oxygen transport through the halocline by turbulent mixing at the basin boundaries, i.e. the location where the halocline gets in the vicinity of the seafloor. We used velocity data from moorings and ship based velocity shear microstructure measurements using a MSS profiler. The data was acquired during three different cruises/seasons in the Eastern Gotland Basin to identify key processes responsible for oxygen mixing events across the strong halocline. The MSS was equipped with a fast oxygen sensor allowing to quantify the vertical oxygen flux. We focused on specific events with inertial waves, mean currents, and topographic waves as major dominating processes. During these events properties such as vertical shear, stratification and oxygen fluxes were analysed. With this information we were able to estimate the potential of the processes for the diapycnal oxygen transport. We found that inertial waves do not contribute much to the overall oxygen flux across the halocline, whereas topographic waves increase the oxygen flux considerably. Also the mean current lead to significant oxygen fluxes under certain shear and stratification conditions, suggesting that further attention should be turned to those.

Coastal zones and estuaries are highly dynamic marine systems subject to anthropogenic pressure and to climaterelated changes. The coastal zone of the Baltic Sea, shaped by extreme seasonality, strong bentho-pelagic coupling, and intense human use, represents a unique model system to study these interactions under accelerating climate change. While extensive research has been conducted on warming, eutrophication, and large scale hypoxia in the region, critical gaps remain in understanding how physical forcing, sediment type, and benthic-pelagic coupling control nutrient turnover, primary production, seed and egg bank dynamics, and the emission of climate-relevant gases under rapidly changing dynamic conditions. The Baltic Sea, with 26 % of its area shallower than 15 m, harbor mostly sandy sediments along the southern coast, but the coastal nutrient filter remains poorly investigated because element fluxes are mostly controlled by advection. Sediments are home for phytoplankton resting stages, but the contribution of seed germination to the development of phytoplankton blooms is unknown. The resting eggs of zooplankton are also deposited in the sediment, but the timing of zooplankton and fish development in spring and the impact of progressive warming are poorly understood. Decreases in salinity strongly influence macrobenthos in the Baltic Sea, whereas increased eutrophication favors the growth of opportunistic species. Finally, coastal darkening is discussed, as it affects marine life in ways that are difficult to assess. Future studies of coastal zones will benefit from technical innovations like mooring systems that transmits data immediately to the shore and uses drones to aid in sampling along coastlines. This review synthesizes current knowledge on the state and functioning of the Baltic coastal zone, highlighting novel insights into the role of permeable sandy sediments as nutrient cycling hotspots. We identify key uncertainties arising from the high spatio-temporal variability of these systems, which limit the predictive capacity of existing models. Only by combining novel approaches we can improve projections of climate-change impacts, and provide a robust scientific basis for the management and protection of vulnerable coastal ecosystems. Accordingly, the measures that will enable stakeholders and politicians to improve the protection of coastal areas remain to be developed.

The Baltic Sea, a European semi-enclosed marginal sea, is driven by the estuarine circulation of dense, saline North-Sea water entering the Baltic Sea and mixing with the freshwater input due to rivers and precipitation. The mixed brackish water leaves the Baltic Sea at the surface through the Danish Belts and the Sound. These processes lead to a strong vertical stratification of the Baltic Sea water masses, the halocline. The slow water exchange causes a mean residence time of the water of 30 years, which leads an accumulation of nutrients. A major consequence of the long residence time and the halocline are low oxygen concentrations below the halocline, with virtually permanent anoxic conditions in the deep basins of the Baltic Sea. To what respect climate change, with the warming of the Baltic Sea as one effect, is impacting the Baltic Sea ecosystem is an open and very relevant research question. One potential consequence could be a further spreading of low or anoxic zones towards the coastal areas, which is already being observed. A less well understood part of the Baltic Sea are the shallow coastal zones, but recent research points to the direction of a strong relevance for e.g. the nutrient turnover. To develop a fundamental understanding of the relevant processes and their coupled effect on the biota, it is therefore essential to measure, monitor and predict the shallow water processes along the margins of the Baltic Sea and how they alter the state of the sea at a basin-wide scale. To address these research questions, the IOW is establishing an interdisciplinary network of long-term and short-term observations in the coastal area of the southern Baltic Sea. This involves deploying moorings in shallow water that send their data to the institute in real time, where they are made immediately available to the general public. The essential ocean parameters (EOP) acquired will be used to control specialized sampling. A measurement program on biogeochemical nutrient turnover, sediment dynamics, geophysics, phytoplankton and zooplankton takes place regularly and is linked to physical data on current patterns, wave intensity and turbulence. The in-Situ measurements are combined with high-resolution numerical modeling to be able to extrapolate the field measurements and to develop numerical experiments. Different stakeholders groups will be involved to provide society and authorities with the latest findings of the measurement campaigns.

Sharp fronts with temperature differences of approximately 0.5°C across a remarkably small lateral scale of order 10 m were observed in a subtropical region with strong mesoscale and submesoscale activity in the southeast Atlantic at 34°S, 6.5°E, far away from any coastal freshwater sources. These fronts were formed at the leading edge of a buoyant gravity current of 20-40 m thickness that propagated at a speed of order 0.1 m/s relative to the colder and thus denser surrounding waters. High-resolution turbulence microstructure observations revealed strongly enhanced turbulence inside the nose of the gravity current, while turbulence in the trailing bulk region was mainly wind- and convectively-driven and showed a strong diurnal modulation. Satellite and meteorological data suggest that the gravity current was triggered by the mesoscale strain-induced sharpening and final collapse of a larger-scale front at the edge of a mesoscale eddy during a period with decaying winds. In contrast to previous studies that have identified similar buoyant gravity currents in the equatorial ocean, our data suggest that they can also form at a mid-latitude location where rotational effects are strong. This suggests that even balanced fronts can decay into gravity currents under certain conditions, indicating a potentially important pathway for mesoscale energy dissipation and mixing.

In this study we used single-model ensemble simulations, generated by perturbed initial conditions, to study the variability in the Baltic Sea. The outcome of each simulation is viewed as one realization of the same stochastic process. The constructed ensemble of simulations reveals a high variability of the 2014/2015 Major Baltic Inflow event, which is not possible to cover with measurement data or an individual model realization. Furthermore, robust analyses of short-term dynamics up to daily temporal scales using the local Water Mass Transformation framework are rendered possible, when combined with single-model ensemble simulations.

As a part of the Scientific Committee on Oceanographic Research (SCOR) Working Group #160 “Analyzing ocean turbulence observations to quantify mixing” (ATOMIX), we have developed recommendations on best practices for estimating the rate of dissipation of kinetic energy, ε, from measurements of turbulence shear using shear probes. The recommendations provided here are platform-independent and cover the conceivable range of dissipation rates in the ocean, seas, and other natural waters. They are applicable to commonly deployed platforms that include vertical profilers, fixed and moored instruments, towed profilers, submarines, self-propelled ocean gliders, and other autonomous underwater vehicles. The procedure for preparing the shear data for spectral estimation is discussed in detail, as are the quality control metrics that should accompany each estimate of ε. The methods are illustrated using a high-quality ‘benchmark’ dataset, while potential pitfalls are demonstrated with a second dataset containing common faults.

Turbulent mixing in the ocean, lakes and reservoirs facilitates the transport of momentum, heat, nutrients, and other passive tracers. Turbulent fluxes are proportional to the rate of turbulent kinetic energy dissipation per unit mass, ε. A common method for ε measurements is using microstructure profilers with shear probes. Such measurements are now widespread, and a non-expert practitioner will benefit from best practice guidelines and benchmark datasets. As a part of the Scientific Committee on Oceanographic Research (SCOR) working group on “Analysing ocean turbulence observations to quantify mixing” (ATOMIX), we compiled a collection of five benchmark data of ε from measurements of turbulence shear using shear probes. The datasets are processed using the ATOMIX recommendations for best practices documented separately. Here, we describe and validate the datasets. The benchmark collection is from different types of instruments and covers a wide range of environmental conditions. These datasets serve to guide the users to test their ε estimation methods and quality-assurance metrics, and to standardize their data for archiving.

In coastal zones, intense organic matter cycling occurs due to land proximity, water – sediment interaction, and exchange processes with the open ocean. Nitrogen sources include atmospheric deposition, submarine groundwater discharge, wetlands, rivers/estuaries and the open ocean. All sources are highly impacted by human activities, such as food production. The nitrogen cycle consists of mostly microbial processes, including nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA), which interact in different ways depending on environmental factors, in particular, the availability of oxygen. At present, human-induced production of reactive nitrogen globally equals the natural one, and a large part of it is introduced into the coastal ocean, where it strongly affects ecology, for example, through eutrophication. In the future, unless anthropogenic nitrogen inputs are reduced, a deterioration of the ecological situation can be expected when rising temperatures and declining oxygen exacerbate the effects of the anthropogenic nitrogen inputs.

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.

Abstract Diapycnal mixing impacts vertical transport rates of salt, heat, and other dissolved substances, essential for the overturning circulation and ecosystem functioning in marine systems. While most studies have focused on mixing induced by individual obstacles in tidal flows, we investigate the net effect of non‐tidal flow over multiple small‐scale (<1 km) bathymetric features penetrating a strongly‐stratified density interface in a coastal region. We combine high‐resolution broadband acoustic observations of turbulence microstructure with traditional shear microstructure profiling, to resolve the variability and intermittency of stratified turbulence related to the rough bathymetry. Scale analysis and acoustic imaging suggest that underlying mixing mechanisms are related to topographic wake eddies and breaking internal waves. Depth averaged dissipation rates (1.1 × 10−7 Wkg−1) and turbulent vertical diffusivities (7 × 10−4 m2s−1) in the halocline exceed reference values by two orders of magnitude. Our study emphasizes the importance of rough small‐scale bathymetric features for the vertical transport of salt in coastal areas.

Benthic oxygen dynamics and the exchange of oxygen and other solutes across the sediment-water interface play a key role for the oxygen budget of many limnic and shallow marine systems. The sediment-water fluxes are largely determined by two factors: sediment biogeochemistry and the thickness of the diffusive boundary layer that is determined by near-bottom turbulence. Here, we present a fully coupled benthic-pelagic modeling system that takes these processes and their interaction into account, focusing especially on the modulation of the sediment-water fluxes by the effects of near-bottom turbulence and stratification. We discuss the special numerical methods required to guarantee positivity and mass conservation across the sediment-water interface in the presence of rapid element transformation, and apply this modeling system to a number of idealized scenarios. Our process-orientedsimulations show that near-bottom turbulence provides a crucial control on the sediment-water fluxes, the oxygen penetration depth, and the re-oxidation of reduced compounds diffusing upward from the deeper benthic layers especially on time scales of a few days, characterizing oceanic tides,internal seiching motions in lakes, and mesoscale atmospheric variability. Our results also show that the response of benthic-pelagic fluxes to rapidchanges in the forcing conditions (e.g., storm events) can only be understood with a fully coupled modeling approach.

Insufficient diapycnal oxygen transport through the halocline is the key reason for the anoxic conditions typically observed in the deeper parts of the Baltic Sea. The variability of turbulent oxygen fluxes through the halocline was investigated seasonally and in space during three cruises (summer, fall, winter). Turbulence dissipation rates and oxygen fluxes showed a pronounced seasonal pattern, with the lowest values during summer. At the basin boundaries, halocline oxygen fluxes increased by an order of magnitude as a result of boundary mixing. A simple box model, distinguishing between interior, intermediate, and boundary regions, was used to extrapolate the locally observed fluxes to the central Baltic Sea. The boundary area, covering less than 23% of the total basin area, contributed more than 80% of the basin‐scale oxygen transport through the halocline. According to this model, the annual oxygen flux through the halocline is of the order of 20–28 Gmol per year.

Stratified oceanic turbulence is strongly intermittent in time and space, and therefore generally underresolved by currently available in situ observational approaches. A promising tool to at least partly overcome this constraint are broadband acoustic observations of turbulent microstructure that have the potential to provide mixing parameters at orders of magnitude higher resolution compared to conventional approaches. Here, we discuss the applicability, limitations, and measurement uncertainties of this approach for some prototypical turbulent flows (stratified shear layers, turbulent flow across a sill), based on a comparison of broadband acoustic observations and data from a free-falling turbulence microstructure profiler. We find that broadband acoustics are able to provide a quantitative description of turbulence energy dissipation in stratified shear layers (correlation coefficient r = 0.84) if the stratification parameters required by the method are carefully preprocessed. Essential components of our suggested preprocessing algorithm are 1) a vertical low-pass filtering of temperature and salinity profiles at a scale slightly larger than the Ozmidov length scale of turbulence and 2) an automated elimination of weakly stratified layers according to a gradient threshold criterion. We also show that in weakly stratified conditions, the acoustic approach may yield acceptable results if representative averaged vertical temperature and salinity gradients rather than local gradients are used. Our findings provide a step toward routine turbulence measurements in the upper ocean from moving vessels by combining broadband acoustics with in situ CTD profiles.

The characteristics of tidal velocity profiles and their relation to stratification are investigated based on high-resolution field data collected at four locations in the German Bight Region of Freshwater Influence (ROFI) in the North Sea. The deployments each include two to three tidal cycles and were conducted during field campaigns in August 2016 and May 2018. The depth-averaged semidiurnal tidal motion is dominated by a standing wave directed toward the coast, but modified by a smaller, coast-parallel progressive wave contribution. The time series of the tidal velocity profiles consistently show tidal asymmetries with higher flood than ebb velocities near the surface and counter-clockwise rotation of the velocity trajectories at depth. Near the surface, phase-locked periodic changes in the sense of rotation within the tidal cycle are evident for three deployments, resulting in periodic counter-rotation of the upper and lower layer. During these episodes, stratification of the water column is observed. Counter-rotation is initiated after a sudden decoupling developing from the surface downward, with subsequent rapid development of stratification and velocity shear. The observed decoupling is most likely triggered by advection of the plume-induced lateral surface density gradient by weakly sheared ebb currents toward the study site. Due to the dominance of the standing wave in the German Bight ROFI, the observed intra-tidal variations of stratification are more similar to the Liverpool Bay and differ significantly from the Rhine ROFI, where the tidal dynamics are controlled by a progressive Kelvin wave.