The paper presents a review of the current state of knowledge regarding the role of the marginal filter and climate in the ecosystem changes of the Black Sea. The marginal filter (MF) is a key buffer zone at the river–sea interface, where the bulk of terrigenous material delivered from land is deposited and transformed. The MF concept was developed by A.P. Lisitsyn, who demonstrated that the five-stage filter in this contact zone retains 93–95% of suspended particulate matter and about 40% of dissolved substances. The study is the first basin-wide synthesis in which the Lisitsyn concept is applied not for local flux calculations, but as an interpretive tool for understanding the cascade of ecosystem collapses across the entire sea, complementing existing local-scale studies of the Black Sea MF. The functioning of the Black Sea MF as an integrated geoecological buffer system remains poorly understood: this sea is distinguished by its extensive shelf, shallow pycnocline, and hydrogen sulphide zone. The limited volume of oxygenated waters, together with the sea’s dependence on river runoff, renders the MF critically important for the ecosystem. The author hypothesises that the destruction of the biological block of the MF in the 1960s–1980s by intensive bottom trawling, which eradicated the Phyllophora field and benthic filter-feeders, triggered a cascading degradation: a disaster on the shelf (1950s–1980s), a disaster in the open sea (1980–1988), and a collapse of the entire ecosystem (1988–2000). However, the shift to a novel state (>2000) is already linked to climate: warming caused the disappearance of the Cold Intermediate Layer (2019), which had harboured boreal relicts – key forage zooplankton taxa and commercial fish species. Further warming will fundamentally alter the Black Sea ecosystem.