Non-exhaustive list.
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Eutrophication is a significant problem in the Baltic Sea, caused by excess nutrients from various sources including agriculture, wastewater and industries. This leads to excessive algae proliferation which depletes oxygen in the water, thus impacting marine flora and fauna.
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Marine pollution linked to industry and maritime transport, leading to discharges of harmful substances such as hydrocarbons and heavy metals, requiring strict management and more rigorous environmental standards to minimize these impacts.
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Plastic pollution in the Baltic Sea, resulting from plastic waste being washed into rivers and threatening marine wildlife. Measures to reduce plastics at the source, along with recycling and awareness, are needed to address this problem.

Acidification of the Baltic Sea due to increased carbon dioxide emissions, harmful to marine organisms and biodiversity, highlighting the importance of reducing CO2 emissions.

Pollution of coastal waters caused by shipping and port activities, involving fuel discharges, accidental spills and sewage. Cleaner port practices and prevention measures are essential to mitigate these impacts.
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Degradation of coastal ecosystems due to unregulated construction, damaging sensitive natural habitats, requiring sustainable urban planning and strict environmental regulations.
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Chemical pollution from industrial activities, causing releases of heavy metals, industrial chemicals and toxic substances into waters. Strengthening environmental regulations and processing industrial waste are necessary to reduce this pollution.
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Impact of offshore oil and gas activities on marine ecosystems, with oil leaks and oil spills causing damage to marine habitats and biodiversity, requiring high safety standards and disaster response measures.
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Overfishing is an additional challenge that threatens the sustainability of marine resources. Overexploitation of fish stocks and other marine species can lead to ecological imbalances, declines in fish populations, and negative economic and social impacts for communities dependent on fishing. Combating overfishing requires effective quota management, protection of marine areas, and promotion of sustainable fishing practices to preserve marine ecosystems in the long term.​