The Sea of Marmara is undergoing a severe marine pollution crisis driven by chronic nutrient enrichment and recurrent mucilage outbreaks. The physical mechanisms controlling transport, accumulation and persistence of pollutants and organic matter remain insufficiently resolved. Here, we quantify how three-dimensional (3D) circulation regulates dispersal and retention in this strongly stratified, semi-enclosed basin. A high-resolution Lagrangian particle-tracking framework forced by the Coastal and Regional Ocean COmmunity model (CROCO) resolves transport pathways and transit times, with particles as proxies for nutrients and suspended organic matter. Comparing ensembles of two-dimensional (2D) and 3D simulations shows that vertical processes, including shear dispersion and episodic subduction, substantially modify particle pathways and delay horizontal transport. In stratified sub-basins, 3D dynamics extend transit times by up to 100 days relative to 2D estimates, so neglecting vertical exchange systematically underestimates how long material is retained. A persistent retention hotspot emerges in the southwestern basin, where mean transit times exceed 250 days. Such conditions favour the prolonged accumulation of suspended organic material, although mucilage formation additionally involves biological and biogeochemical processes that passive particles do not represent. Lagrangian probability density functions show that dispersal converges on persistent retention areas that recur across release years and release regions, while the rate of accumulation varies between years. These results establish a mechanistic link between 3D circulation and the spatial organization of pollution retention, with implications for monitoring design and mitigation in the Sea of Marmara and analogous stratified semi-enclosed seas.
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