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Climate change has multiple direct and indirect potentially synergistic effects on Baltic Sea species, organism communities, and on ecosystem functioning, through 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. Evidence on effects of climate are compiled from and reviewed for field studies, experimental work, as well as modelling studies primarily from published literature after 2010. The responses vary within and between species groups, even between sibling species. Such subtle differences, as well as secondary feedbacks and altered trophic pathways, make projections difficult. Some common patterns arise from the wealth of recent studies, however. It is likely that the combined effects of increased external nutrient loads, stratification and internal loading will improve the conditions for cyanobacterial blooms in large parts of the Baltic. In the northernmost areas the increasing allochtonous DOM may further complicate the picture by increasing heterotrophy and by decreasing food web efficiency. This effect may, however, be counteracted by the intensification of the bacteria-flagellate-microzooplankton-mesozooplankton link, which may change the system from a bottom-up controlled one to a top-down controlled one. In deep benthic communities, continued eutrophication may promote higher sedimentation of organic matter and increase zoobenthic biomasses, but eventually increasing stratification and hypoxia/anoxia will disrupt benthic-pelagic coupling, leading to reduced benthic biomass. In the photic benthic systems warmer winters with less ice and nutrient increase enhances eutrophication. The projected salinity decline suppresses marine species, and temperature increase overgrowth of perennial macroalgae by annual filamentous alga throughout the growing-season, and major changes in the marine entire ecosystem are expected. The changes in environmental conditions probably also lead to increased establishment of non-indigenous species, potentially affecting food web dynamics in large areas of the Baltic Sea. However, several modelling studies have concluded that nutrient reductions according to the Baltic Sea Action Plan of Helsinki Commission may be a stronger driver for ecosystem functions in the Baltic Sea than climate change. Such studies highlight the importance of studying the Baltic Sea as an interlinked socio-ecological system. Knowledge gaps include uncertainties in projecting the future salinity level as well as stratification under different climate forcings. This weakens our ability to project how overall biodiversity, pelagic productivity, fish populations, and macroalgal communities may change in the future. Experimental work must be better integrated into 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. Few studies have holistically investigated the shallow water ecosystems holistically. There are complex climate-induced interactions and multiple feedbacks between algae, grazers and their predators, that are poorly known, as are the effects of non-native invasive species. Finally, both 2D species distribution models and 3D ecosystem models could benefit from better integration of approaches including physical, chemical and biological parameters. [ABSTRACT FROM AUTHOR]