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We demonstrate changes in ecosystem stable states in a coastal lagoon that are consistent with what a regime shift would hypothesize. In the nutrient-stressed Ringkøbing Fjord, Denmark, a small change in one variable (salinity) facilitated by a change in sluice management, caused a sudden regime shift from a bottom-up controlled turbid state, into a top-down controlled clear-water state. The change in dominating pathway of organic matter production from pelagic turnover to benthic-pelagic coupling was facilitated by new recruitment and growth of existing suspension-feeding clams, Mya arenaria. With the invasion of clams, benthic grazing became the key feature of the biological structure. Phytoplankton composition and zooplankton abundance were also affected by the change in biological structure. The small, but sudden, increase in salinity caused by the change in sluice management led to a dramatic reduction in biomass and coverage of benthic vegetation and thus affected herbivorous waterbird populations. In recent years, plant coverage has been increasing, as can be expected with increased water transparency. The regime shift has some major implications for coastal water management and revealed some conflicts between different types of nature and environmental protection legislation.