Climate change has multiple effects on Baltic Sea species, communities and ecosystem functioning through changes in physical and biogeochemical environmental characteristics of the sea. Associated indirect and secondary effects on species interactions, trophic dynamics and ecosystem function are expected to be significant. We review studies investigating species-, population- and ecosystem-level effects of abiotic factors that may change due to global climate change, such as temperature, salinity, oxygen, pH, nutrient levels, and the more indirect biogeochemical and food web processes, primarily based on peer-reviewed literature published since 2010. For phytoplankton, clear symptoms of climate change, such as prolongation of the growing season, are evident and can be explained by the warming, but otherwise climate effects vary from species to species and area to area. Several modelling studies project a decrease of phytoplankton bloom in spring and an increase in cyanobacteria blooms in summer. The associated increase in N : P ratio may contribute to maintaining the "vicious circle of eutrophication". However, uncertainties remain because some field studies claim that cyanobacteria have not increased and some experimental studies show that responses of cyanobacteria to temperature, salinity and pH vary from species to species. An increase of riverine dissolved organic matter (DOM) may also decrease primary production, but the relative importance of this process in different sea areas is not well known. Bacteria growth is favoured by increasing temperature and DOM, but complex effects in the microbial food web are probable. Warming of seawater in spring also speeds up zooplankton growth and shortens the time lag between phytoplankton and zooplankton peaks, which may lead to decreasing of phytoplankton in spring. In summer, a shift towards smaller-sized zooplankton and a decline of marine copepod species has been projected. In deep benthic communities, continued eutrophication promotes high sedimentation and maintains good food conditions for zoobenthos. If nutrient abatement proceeds, improving oxygen conditions will first increase zoobenthos biomass, but the subsequent decrease of sedimenting matter will disrupt the pelagic-benthic coupling and lead to a decreased zoobenthos biomass. In the shallower photic systems, heatwaves may produce eutrophication-like effects, e.g. overgrowth of bladderwrack by epiphytes, due to a trophic cascade. If salinity also declines, marine species such as bladderwrack, eelgrass and blue mussel may decline. Freshwater vascular plants will be favoured but they cannot replace macroalgae on rocky substrates. Consequently invertebrates and fish benefiting from macroalgal belts may also suffer. Climate-induced changes in the environment also favour establishment of non-indigenous species, potentially affecting food web dynamics in the Baltic Sea. As for fish, salinity decline and continuing of hypoxia is projected to keep cod stocks low, whereas the increasing temperature has been projected to favour sprat and certain coastal fish. Regime shifts and cascading effects have been observed in both pelagic and benthic systems as a result of several climatic and environmental effects acting synergistically. Knowledge gaps include uncertainties in projecting the future salinity level, as well as stratification and potential rate of internal loading, under different climate forcings. This weakens our ability to project how pelagic productivity, fish populations and macroalgal communities may change in the future. The 3D ecosystem models, food web models and 2D species distribution models would benefit from integration, but progress is slowed down by scale problems and inability of models to consider the complex interactions between species. Experimental work should be better integrated into empirical and modelling studies of food web dynamics to get a more comprehensive view of the responses of the pelagic and benthic systems to climate change, from bacteria to fish. In addition, to better understand the effects of climate change on the biodiversity of the Baltic Sea, more emphasis should be placed on studies of shallow photic environments. The fate of the Baltic Sea ecosystem will depend on various intertwined environmental factors and on development of the society. Climate change will probably delay the effects of nutrient abatement and tend to keep the ecosystem in its "novel" state. However, several modelling studies conclude that nutrient reductions will be a stronger driver for ecosystem functioning of the Baltic Sea than climate change. Such studies highlight the importance of studying the Baltic Sea as an interlinked socio-ecological system.
