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This article analyzes scrubber systems as a temporary solution that emerged in response to the IMO 2020 environmental requirements for limiting sulfur content in marine fuel. The authors approach the topic from a broader perspective, applying an integrated environmental vision known as Earth system thinking. Instead of focusing solely on reducing air emissions, the study points to the effect of transferring pollution from the atmosphere to the sea through the discharge of wash water. This phenomenon is called the “Scrubber Paradox”: a situation in which a reduction in one type of pollution (SOx in the air) leads to an increase in another (chemical load on the marine environment). Particular attention is paid to the risks to coastal and enclosed seas, such as the Black Sea, where discharges can have a long-term impact on the marine ecosystem. The paper emphasizes that formal compliance with air standards does not guarantee overall environmental safety. Current environmental policies often remain narrow in scope, focusing only on the atmosphere and ignoring the marine environment, which leads to spatial and social asymmetries: some regions reap the benefits (cleaner air), while others bear the environmental burden (polluted waters). Therefore, scrubbing technologies should not be considered as a definitive solution to environmental problems, but rather as a transitional tool that allows time to be gained for the implementation of more sustainable solutions. In the long term, an integrated approach to environmental policy and a gradual transition to environmentally safe shipping is needed, which does not eliminate one threat by creating another.