The coastal zone of the Baltic Sea is diverse with strong regional differences in the physico-chemical setting. This diversity is also reflected in the importance of different biogeochemical processes altering nutrient and organic matter fluxes on the passage from land to sea. This review investigates the most important processes for removal of nutrients and organic matter, and the factors that regulate the efficiency of the coastal filter. Nitrogen removal through denitrification is high in lagoons receiving large inputs of nitrate and organic matter. Phosphorus burial is high in archipelagos with substantial sedimentation, but the stability of different burial forms varies across the Baltic Sea. Organic matter processes are tightly linked to the nitrogen and phosphorus cycles. Moreover, these processes are strongly modulated depending on composition of vegetation and fauna. Managing coastal ecosystems to improve the effectiveness of the coastal filter can reduce eutrophication in the open Baltic Sea.

The Curonian Lagoon, the largest in Europe, suffers from nuisance cyanobacterial blooms during summer, probably triggered by unbalanced nutrient availability. However, nutrient delivery to this system was never analysed in detail. During 2012–2016, we analysed the monthly discharge, nutrient loads, and ecological stoichiometry at the closing section of the Nemunas River, the main nutrient source to the lagoon. The aim of this study was to investigate seasonal and annual variations of nitrogen (N), silica (Si), and phosphorous (P) with respect to discharge, climatic features, and historical trends. The nutrient loads varied yearly by up to 50% and their concentrations underwent strong seasonality, with summer N and Si limitation. The river discharge (16 ± 4 km³·yr⁻¹) was lower than the historical average (21.8 km³·yr⁻¹). Changes in agricultural practices resulted in similar N export from the river watershed compared to historical data (1986–2002), while sewage treatment plant improvements led to a ~60% decrease of P loads. This work contributes new data to the scattered available information on the most important nutrient source to the Curonian Lagoon. Further P reduction is needed to avoid unbalanced dissolved inorganic nitrogen and phosphorus (DIN:DIP~10) ecological stoichiometry in summer, which may stimulate undesired cyanobacterial blooms.

Mangrove forests are among the most productive and diverse ecosystems on the planet, despite limited nitrogen (N) availability. Under such conditions, animal-microbe associations (holobionts) are often key to ecosystem functioning. Here, we investigated the role of fiddler crabs and their carapace-associated microbial biofilm as hotspots of microbial N transformations and sources of N within the mangrove ecosystem. 16S rRNA gene and metagenomic sequencing provided evidence of a microbial biofilm dominated by Cyanobacteria, Alphaproteobacteria, Actinobacteria, and Bacteroidota with a community encoding both aerobic and anaerobic pathways of the N cycle. Dinitrogen (N₂) fixation was among the most commonly predicted process. Net N fluxes between the biofilm-covered crabs and the water and microbial N transformation rates in suspended biofilm slurries portray these holobionts as a net N₂ sink, with N₂ fixation exceeding N losses, and as a significant source of ammonium and dissolved organic N to the surrounding environment. N stable isotope natural abundances of fiddler crab carapace-associated biofilms were within the range expected for fixed N, further suggesting active microbial N₂ fixation. These results extend our knowledge on the diversity of invertebrate-microbe associations, and provide a clear example of how animal microbiota can mediate a plethora of essential biogeochemical processes in mangrove ecosystems.

Estuaries are biogeochemical reactors able to modulate the transfer of energy and matter from the watershed to the coastal zones and to retain or remove large amounts of terrestrially generated nutrients. However, they may switch from nutrient sink to source depending upon interannual variability of the nutrient supply and internal processes driving whole system metabolism (e.g., net autotrophic or heterotrophic). We tested this hypothesis in the Curonian Lagoon, a hypertrophic estuary located in the south east Baltic Sea, following the budget approach developed in the Land-Ocean Interactions in the Coastal Zone (LOICZ) project. Annual budgets for nitrogen (N), phosphorus (P), and silica (Si) were calculated for the 2013–2015 period. The lagoon was divided in a flushed, nutrient loaded area, and in a confined, less loaded area. The lagoon was always a sink for dissolved inorganic Si and P whereas it was a N sink in the confined area, dominated by denitrification, and a N source in the flushed area, due to dinitrogen (N₂) fixation. The net ecosystem metabolism (NEM) indicated that the Curonian Lagoon was mainly autotrophic because of high primary production rates. In this turbid system, low N:P ratio, high summer temperatures, and calm weather conditions support high production of N₂-fixing cyanobacteria, suppressing the estuarine N-sink role.

Under current circumstances, coastal lagoons are net emitters of nitrous oxide (N₂O) to the atmosphere. We hypothesize that widespread nitrogen‐driven coastal eutrophication will enhance N₂O production and emissions from coastal lagoons. Here, we quantified spatial and temporal patterns of sediment‐water and water‐air N₂O fluxes in three large eutrophic lagoons in Europe. Annual sediment N₂O fluxes ranged between −0.3 ± 0.3 (summer) and 10.6 ± 2.0 μmol m⁻² d⁻¹ (spring). In spring, conspicuous sediment effluxes were mainly supported by high nitrate concentrations (89–202 μM) and incomplete denitrification. In summer, a small sediment influx was related to nitrate limitation (0–9 μM), potentially leading to N₂O demand for denitrification. The water‐air N₂O fluxes were comparable with benthic fluxes, indicating that sediment was the main source of N₂O to the atmosphere. The hypereutrophic Curonian Lagoon had the largest N₂O emission at 4.9 ± 2.1 μmol m⁻² d⁻¹, while the less eutrophic Oder and Vistula lagoons emitted 2.5 ± 1.0 and 2.0 ± 0.7 μmol m⁻² d⁻¹, respectively. Our observations, combined with earlier measurements in coastal lagoons worldwide, revealed a lagoon median (Q1–Q3) N₂O emission of 14.2 (2.7–29.8) Gg yr⁻¹, which is about 48% higher than previous estimates. Eutrophication driven by large nitrogen inputs is thus a significant driver of coastal N₂O emissions globally.