Marine management involves assessing risks to natural and human systems and implementing measures to mitigate them. Eutrophication, driven by excess nutrients and organic matter, is a major risk in the Black Sea, largely caused by agricultural runoff, urban wastewater, maritime transport, and climate change. This study uses Bow-tie Analysis (BTA) and FCM (Fuzzy Cognitive Maps) to evaluate three IPCC-based management scenarios—Sustainable Future, Moderate Progress, and Deteriorating Conditions—to address eutrophication. These scenarios were assessed for their effectiveness in reducing nutrient runoff, improving water quality, and achieving Good Environmental Status (GES) under Descriptor 5 of the EU Marine Strategy Framework Directive. Key pressures such as agriculture, wastewater, shipping, and low public awareness were linked to targeted controls, including technological improvements, adaptive legislation, and enhanced public engagement. Results show that proactive and integrated measures in the Sustainable Future scenario substantially improve water quality. The Moderate Progress scenario reflects limited success, with some ongoing challenges. The Deteriorating Conditions scenario underscores the risks of weak control measures and policy inaction. The study highlights the importance of coordinated management strategies, adequate policy support, and stakeholder involvement to ensure the Black Sea’s ecological resilience—offering valuable insights for other vulnerable semi-enclosed marine systems. Keywords: Bow-tie Analysis, Fuzzy Cognitive Maps, Water Quality, Environmental Management, Black Sea