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.

Based on the Baltic Earth Assessment Reports of this thematic issue in Earth System Dynamics and recent peer-reviewed literature, current knowledge of the effects of global warming on past and future changes in climate of the Baltic Sea region is summarised and assessed. The study is an update of the Second Assessment of Climate Change (BACC II) published in 2015 and focuses on the atmosphere, land, cryosphere, ocean, sediments, and the terrestrial and marine biosphere. Based on the summaries of the recent knowledge gained in palaeo-, historical, and future regional climate research, we find that the main conclusions from earlier assessments still remain valid. However, new long-term, homogenous observational records, for example, for Scandinavian glacier inventories, sea-level-driven saltwater inflows, so-called Major Baltic Inflows, and phytoplankton species distribution, and new scenario simulations with improved models, for example, for glaciers, lake ice, and marine food web, have become available. In many cases, uncertainties can now be better estimated than before because more models were included in the ensembles, especially for the Baltic Sea. With the help of coupled models, feedbacks between several components of the Earth system have been studied, and multiple driver studies were performed, e.g. projections of the food web that include fisheries, eutrophication, and climate change. New datasets and projections have led to a revised understanding of changes in some variables such as salinity. Furthermore, it has become evident that natural variability, in particular for the ocean on multidecadal timescales, is greater than previously estimated, challenging our ability to detect observed and projected changes in climate. In this context, the first palaeoclimate simulations regionalised for the Baltic Sea region are instructive. Hence, estimated uncertainties for the projections of many variables increased. In addition to the well-known influence of the North Atlantic Oscillation, it was found that also other low-frequency modes of internal variability, such as the Atlantic Multidecadal Variability, have profound effects on the climate of the Baltic Sea region. Challenges were also identified, such as the systematic discrepancy between future cloudiness trends in global and regional models and the difficulty of confidently attributing large observed changes in marine ecosystems to climate change. Finally, we compare our results with other coastal sea assessments, such as the North Sea Region Climate Change Assessment (NOSCCA), and find that the effects of climate change on the Baltic Sea differ from those on the North Sea, since Baltic Sea oceanography and ecosystems are very different from other coastal seas such as the North Sea. While the North Sea dynamics are dominated by tides, the Baltic Sea is characterised by brackish water, a perennial vertical stratification in the southern subbasins, and a seasonal sea ice cover in the northern subbasins.

Even though the effects of benthic fauna on aquatic biogeochemistry have been long recognized, few studies have addressed the combined effects of animal bioturbation and metabolism on ecosystem–level carbon and nutrient dynamics. Here we merge a model of benthic fauna (BMM) into a physical–biogeochemical ecosystem model (BALTSEM) to study the long-term and large-scale effects of benthic fauna on nutrient and carbon cycling in the Baltic Sea. We include both the direct effects of faunal growth and metabolism and the indirect effects of its bioturbating activities on biogeochemical fluxes of and transformations between organic and inorganic forms of carbon (C), nitrogen (N), phosphorus (P) and oxygen (O). Analyses of simulation results from the Baltic Proper and Gulf of Riga indicate that benthic fauna makes up a small portion of seafloor active organic stocks (on average 1 %–4 % in 2000–2020) but contributes considerably to benthic–pelagic fluxes of inorganic C (23 %–31 %), N (42 %–51 %) and P (25 %–34 %) through its metabolism. Results also suggest that the relative contribution of fauna to the mineralization of sediment organic matter increases with increasing nutrient loads. Further, through enhanced sediment oxygenation, bioturbation decreases benthic denitrification and increases P retention, the latter having far-reaching consequences throughout the ecosystem. Reduced benthic–pelagic P fluxes lead to a reduction in N fixation and primary production, lower organic matter sedimentation fluxes, and thereby generally lower benthic stocks and fluxes of C, N and P. This chain of effects through the ecosystem overrides the local effects of faunal respiration, excretion and bioturbation. Due to large uncertainties related to the parameterization of benthic processes, we consider this modelling study a first step towards disentangling the complex ecosystem-scale effects of benthic fauna on biogeochemical cycling.

Explaining the recent decline of eastern Baltic cod (EBC) remains scientifically challenging. Brander proposes in a comment to Svedäng et al.that the observed trend in oxygen in SD 25 supports the idea that juvenile cod are balancing the physiological cost of living under mild hypoxiaby offsetting the risk of being eaten by diving seals and cormorants in shallower water with more oxygen. There are a number of objections tothis conjecture, besides the fact that supporting observations are missing. Hence, it is difficult to reconcile the long-term development of EBCunder varying oxygen conditions with the hypothesis that a small reduction in oxygen content can explain the current strong and uniform declinein growth observed in the entire southern Baltic Sea.

Hypoxia is presently seen as the principal driver behind the decline of the former dominating Eastern Baltic cod stock (EBC; Gadus morhua). It has been proposed that both worsening conditions for reproduction and lower individual growth, condition, and survival are linked to hypoxia. Here, we elucidate the ecological envelope of EBC in terms of salinity stratification, oxygen content, and benthic animal biomasses, and how it has affected EBC productivity over time. The spawning conditions started deteriorating in the Gotland Deep in the 1950s due to oxygen depletion. In contrast, in the Bornholm Basin, hydrographic conditions have remained unchanged over the last 60 years. Indeed, the current extent of both well-oxygenated areas and the frequency of hypoxia events do not differ substantially from periods with high EBC productivity in the 1970s–1980s. Furthermore, oxygenated and therefore potentially suitable feeding areas are abundant in all parts of the Baltic Sea, and our novel analysis provides no evidence of a reduction in benthic food sources for EBC over the last 30 years. We find that while reproduction failure is intricately linked to hydrographic dynamics, a relationship between the spread of hypoxia and the decline in EBC productivity during the last decades cannot be substantiated. 

Despite a wide-ranging research, there is almost no information regarding the major biogeochemical fluxes that could characterize the past and present state of the European Lake Onego ecosystem and be used for reliable prognostic estimates of its future. To enable such capacity, we adapted and implemented a three-dimensional coupled hydrodynamical biogeochemical model of the nutrient cycles in Lake Onego. The model was used to reconstruct three decades of Lake Onego ecosystem dynamics with daily resolution on a 2 × 2 km grid. A comparison with available information from Lake Onego and other large boreal lakes proves that this hindcast is plausible enough to be used as a form of reanalysis. This model will be used as a form of studies of Lake Onego ecosystem, including long-term projections of ecosystem evolution under different scenarios of climate change and socio-economic development.

Несмотря на многолетние широкомасштабные исследования Онежского озера, практически отсутствует информация об основных биогеохимических потоках, которая могла бы характеризовать прошлое и настоящее состояние его экосистемы и использоваться для надежных прогнозных оценок ее будущего. С целью восполнения недостающей информации о состоянии Онежского озера была разработана трехмерная эко-гидродинамическая модель биогеохимического круговорота питательных веществ. Модель использовалась для реконструкции динамики экосистемы Онежского озера за три десятилетия с суточным разрешением на пространственной расчетной сетке 2 × 2 км. Сравнение с имеющейся информацией по Онежскому озеру и другим крупным бореальным озерам доказывает, что этот ретроспектив ный анализ достаточно правдоподобен для оценки изменений в экосистеме озера в современный период. Разработанная модель будет использоваться для исследования экосистемы Онежского озера, включая долгосрочные прогнозы эволюции экосистемы при различных сценариях изменения климата и социально-экономического развития.

A three-dimensional coupled hydrodynamical biogeochemical model of the nitrogen and phosphorus cycles has been used for a long-term reanalysis of the Lake Onego ecosystem. The comparison between simulation and sparse irregular observations, presented in the first part of this paper, demonstrated plausibility of the reconstructed temporal and spatial features of biogeochemical dynamics at a long-term scale, while seasonal dynamics of variables and fluxes are presented here. As new regional phenological knowledge, the reanalysis quantifies that the spring phytoplankton bloom, previously overlooked, reaches a maximum of 500 ± ± 128 mg C m-2 d-1 in May, contributes to approximately half of the lake's annual primary production of 17.0-20.6 g C m-2 yr-1, and is triggered by increasing light availability rather than by an insignificant rise in water temperature. Coherent nutrient budgets provide reliable estimates of phosphorus and nitrogen residence times of 47 and 17 years, respectively. The shorter nitrogen residence time is explained by sediment denitrification, which in Lake Onego removes over 90 % of the bioavailable nitrogen input, but is often ignored in studies of other large lakes. An overall assessment of the model performance allows us considering the model a necessary and reliable tool for scenario simulations of possible changes in the Lake Onego ecosystem at the requested spatial and temporal scales. 

Для многолетнего реанализа экосистемы Онежского озера была использована трехмерная объединенная гидродинамическая биогеохимическая модель круговоротов азота и фосфора. Сопоставление моделирования и разрозненных нерегулярных наблюдений, представленное в первой части статьи, продемонстрировало достоверность восстановленных временных и пространственных особенностей биогеохимической динамики в многолетнем масштабе. В данной работе представлена сезонная динамика компонентов экосистемы и биогеохимических потоков. В качестве новой региональной фенологической информации дана количественная оценка весеннего цветения фитопланктона, которое ранее упускалось из виду, но достигает максимума 500 ± 128 мгC м–2 сут–1 в мае, что составляет примерно половину годовой первичной продукции озера в размере 17,0–20,6. гC м–2 год‑1, и вызывается увеличением доступности света, а не незначительным повышением температуры воды. Когерентные балансы питательных веществ обеспечивают надежные оценки времени пребывания фосфора и азота в 47 и 17 лет соответственно. Более короткое время пребывания азота объясняется денитрификацией отложений, которая в Онежском озере удаляет более 90 % биодоступного поступления азота, но часто игнорируется при исследованиях других крупных озер. Общая оценка работоспособности модели позволяет считать ее необходимым и надежным инструментом для сценарного моделирования возможных изменений экосистемы Онежского озера в требуемых пространственных и временных масштабах.

The fate of microplastics (MP) in seawater is heavily influenced by the biota: the density of MP particles can be changed due to biofouling, which affects sinking, or MP can be digested by zooplankton and transferred into fecal pellets with increased sinking rate. We hypothesize that seasonal production and degradation of organic matter, and corresponding changes in the plankton ecosystem affect the MP capacity for transportation and burying in sediments in different seasons. This is simulated with a coupled hydrodynamical-biogeochemical model that provides a baseline scenario of the seasonal changes in the planktonic ecosystem and changes in the availability of particulate and dissolved organic matter. In this work, we use a biogeochemical model OxyDep that simulates seasonal changes of phytoplankton (PHY), zooplankton (HET), dissolved organic matter (DOM) and detritus (POM). A specifically designed MP module considers MP particles as free particles (MP_free), particles with biofouling (MP_biof), particles consumed by zooplankton (MP_het) and particles in detritus, including fecal pellets (MP_det). A 2D coupled benthic-pelagic vertical transport model 2DBP was applied to study the effect of seasonality on lateral transport of MP and its burying in the sediments. OxyDep and MP modules were coupled with 2DBP using Framework for Aquatic Biogeochemical Modelling (FABM). A depletion of MP from the surface water and acceleration of MP burying in summer period compared to the winter was simulated numerically. The calculations confirm the observations that the “biological pump” can be one of the important drivers controlling the quantity and the distribution of MP in the water column.

Modern models of the Baltic Sea eutrophication describe only a bioavailable fraction of the nutrient input from land, thus introducing uncertainty into forcing. In order to alleviate this uncertainty, the coupled 3D hydrodynamical-biogeochemical St. Petersburg Eutrophication Model (SPBEM) has been expanded with variables representing dissolved organic nutrients. The model modification involves an explicit description of the labile and refractory fractions of dissolved organic nitrogen and phosphorus, in addition to their particulate forms, represented by the detritus variables. The modified SPBEM-2 allows for a full account of the total amounts of nutrients reported in field measurements and presented in environmental documents. Particularly, a model description of detritus, as the only bulk organic matter variable, has been replaced by more realistic parameterizations with adequate rates of settling and mineralization. The extensive validation and verification of the model performance in the Gulf of Finland from 2009 to 2014, based on over 4000 oceanographic stations, shows that SPBEM-2 plausibly reproduces all the major large-scale features and phenomena of the ecosystem dynamics in the Gulf of Finland, especially in its surface productive layer. These demonstrated capabilities of SPBEM-2 make the model a useful tool, both in studies of biogeochemical interactions and in historical and scenario simulations.

Massive cyanobacteria blooms occur almost every summer in the Baltic Sea but the capability to quantitatively predict their extent and intensity is poorly developed. Here we analyse statistical relationships between multi-decadal satellite-derived time series of the frequency of cyanobacteria surface accumulations (FCA) in the central Baltic Sea Proper and a suite of environmental variables. Over the decadal scale (similar to 5-20 years) FCA was highly correlated (R-2 similar to 0.69) with a set of biogeochemical variables related to the amount of phosphorus and hypoxia in bottom layers. Water temperature in the surface layer was also positively correlated with FCA at the decadal scale. In contrast, the inter-annual variations in FCA had no correlation with the biogeochemical variables. Instead, significant correlations were found with the solar shortwave direct flux in July and the sea-surface temperature, also in July. It thus appears that it is not possible to predict inter-annual fluctuations in cyanobacteria blooms from water chemistry. Moreover, environmental variables could only explain about 45% of the inter-annual variability in FCA, probably because year-to-year variations in FCA are significantly influenced by biological interactions.