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Vegetation communities, morphometric and water quality variables were sampled in 62 undisturbed coastal lagoons along a natural land-uplift gradient in the northern Baltic Sea. The lagoons had a morphological inlet threshold reflecting habitat isolation (i.e. the diminished connectedness of the lagoon to the sea) and located in different parts of the archipelago (corresponding to altering wave exposure). We used indirect multivariate methods to find changes in vegetation composition, and axes derived from the analyses were used in correlation and stepwise multiple regression analyses together with environmental variables. Habitat isolation proved to be the strongest predictor for vegetation composition. To identify significant change-points we used a method, which detects regime shifts by accounting for differences in chronological series and gives a regime shift index. Significant shifts in habitat isolation, average depth and total nitrogen were followed by shifts in species variables (i.e. dominant species, cover and species richness) and salinity, total phosphorus and turbidity. Of the species, especially Chara tomentosa showed a shift of high magnitude. Also a shift in wave exposure mirroring position of lagoons in the archipelago structured the species, but this division was seen only for less isolated lagoons. Our results suggest that lagoons are primarily structured by habitat isolation forming two structurally different regimes: one of less isolated lagoons dominated by a diverse array of vascular plants and marine algae of both outer and inner archipelago characters, and one with isolated lagoons dominated by high vegetation cover and dominance of Chara. In addition, vegetation seemed to stabilize water quality in the isolated regime by reducing turbidity and phosphorus, indicating a potential feed-back mechanism and a shift in structuring disturbances from abiotic to biotic factors with habitat isolation.