The observation that ecosystems can undergo abrupt shifts between alternative stable states is conceptually accepted but models capable of describing such phenomena are scarce and mostly confined to theoretical studies. The Ringkøbing Fjord is a coastal lagoon where a regime shift was observed in 1996 after changing the sluice-gate practice, manifested through a multitude of ecosystem responses with different dynamics and time lags. Non-linear time series models were developed to describe the interaction between various ecosystem components. The objective was to identify critical threshold values for maintaining the present state and to investigate the ecosystem resilience through stochastic perturbations. The analysis documented three different regime shifts between the components: 1) a salinity threshold allowing clams to settle, 2) salinity thresholds for two different benthic vegetation types, and 3) a flip-flop between nitrogen and phosphorus limitation caused by increased capacity to iron-bind phosphate in the sediments. The model was used to assess different scenarios for managing the lagoon including both the hydraulic control and nutrient discharges.