Hypoxia is a well-described phenomenon in the offshore waters of the Baltic Sea with both the spatial extent and intensity of hypoxia known to have increased due to anthropogenic eutrophication, however, an unknown amount of hypoxia is present in the coastal zone. Here we report on the widespread unprecedented occurrence of hypoxia across the coastal zone of the Baltic Sea. We have identified 115 sites that have experienced hypoxia during the period 1955–2009 increasing the global total to ca. 500 sites, with the Baltic Sea coastal zone containing over 20% of all known sites worldwide. Most sites experienced episodic hypoxia, which is a precursor to development of seasonal hypoxia. The Baltic Sea coastal zone displays an alarming trend with hypoxia steadily increasing with time since the 1950s effecting nutrient biogeochemical processes, ecosystem services, and coastal habitat.

Hypoxia has occurred intermittently over the Holocene in the Baltic Sea, but the recent expansion from less than 10 000 km2 before 1950 to >60 000 km2 since 2000 is mainly caused by enhanced nutrient inputs from land and atmosphere. With worsening hypoxia, the role of sediments changes from nitrogen removal to nitrogen release as ammonium. At present, denitrification in the water column and sediments is equally important. Phosphorus is currently buried in sediments mainly in organic form, with an additional contribution of reduced Fe-phosphate minerals in the deep anoxic basins. Upon the transition to oxic conditions, a significant proportion of the organic phosphorus will be remineralized, with the phosphorus then being bound to iron oxides. This iron-oxide bound phosphorus is readily released to the water column upon the onset of hypoxia again. Important ecosystems services carried out by the benthic fauna, including biogeochemical feedback-loops and biomass production, are also lost with hypoxia. The results provide quantitative knowledge of nutrient release and recycling processes under various environmental conditions in support of decision support tools underlying the Baltic Sea Action Plan.

This study provides an inventory of the recent benthic macrofaunal communities in the entire Baltic Sea. The analyses of soft-bottom benthic invertebrate community data based on over 7000 locations in the Baltic Sea suggested the existence of 10 major communities based on species abundances and 17 communities based on species biomasses, respectively. The low-saline northern Baltic, characterized by silty sediments, is dominated by Monoporeia affinis, Marenzelleria spp., and Macoma balthica. Hydrobiidae, Pygospio elegans, and Cerastoderma glaucum dominate the community in sandy habitats off the Estonian west coast and in the southeastern and southern Baltic Sea. Deep parts of the Gulf of Finland and central Baltic Sea often experience hypoxia, and when oxygen levels in these regions recover, Bylgides sarsi was the first species to colonize. The southwestern Baltic Sea, with high salinity, has higher macrofaunal diversity compared with the northern parts. To spatially interpolate the distribution of the major communities, we used the Random Forest method. Substrate data, bathymetric maps, and modelled hydrographical fields were used as predictors. Model predictions were in good agreement with observations, quantified by Cohen's κ of 0.90 for the abundance and 0.89 in the wet weight-based model. Misclassifications were mainly associated with uncommon classes in regions with high spatial variability. Our analysis provides a detailed baseline map of the distribution of benthic communities in the Baltic Sea to be used both in science and management.

In the Helsinki Commission Red List project 2009-2012, taxonomic and distributional data of benthic (macro) invertebrates were compiled by the present authors in a comprehensive checklist of the Baltic Sea fauna. Based on the most recent and comprehensive data, this paper presents the diversity patterns observed among benthic invertebrates in the Baltic Sea. As expected, the total number of species per sub-region generally declined along the salinity gradient from the Danish Straits to the northern Baltic Sea. This relationship is well known from the Baltic Sea and has resulted in a general assumption of an exponentially positive relationship between species richness and salinity for marine species, and a negative relationship for freshwater species. In 1934, Remane produced a diagram to describe the hypothetical distribution of benthic invertebrate diversity along a marine-freshwater salinity gradient. Our results clearly indicated the validity of this theory for the macrozoobenthic diversity pattern within the Baltic Sea. Categorisation of sub-regions according to species composition showed both separation and grouping of some sub-regions and a strong alignment of similarity patterns of zoobenthic species composition along the salinity gradient.

An increase of xenodiversity in plankton and benthos in the eastern Gulf of Finland was observed from 1998 to 2004. Nonindigenous species account for 4.8% of all species found and up to 96% of total biomass. Invasive benthic omnivores, the alien amphipods Gmelinoides fasciatus and Pontogammarus robustoides and the predaceous fish Perccottus glenii with their versatile diets strongly affect the community structure. Invasive sessile seston-feeders that directly (through grazing and water clearance) and indirectly (through recycling of nutrients) interact with other ecosystem components, are mainly represented by the zebra mussel Dreissena polymorpha, which affect the structure of benthic and planktonic communities as well as benthicpelagic coupling. The invasive predatory cladocerans Cercopagis pengoi and Evadne anonyx and larvae of D. polymorpha are only temporary components in the zooplankton, which is limiting their overall effect. Alien benthic bioturbators, the polychaetes Marenzelleria neglecta and the oligochaete Tubificoides pseudogaster account for a high proportion of total abundance and biomass but their effects on native species need further research.