Seasonal succession of the phytoplankton was followed weekly in the eastern and western parts of the Oosterschelde estuary, before (1982–1983) and during (1984–1986) the construction of the storm-surge barrier. Construction of the barrier seriously influenced the hydrodynamics of the estuary. In the eastern part, decreased current velocities led to the emergence of a vertical salinity gradient, to an increasing sedimentation of suspended matter and to a rise in transparency during a prolonged period of the year. The relationship between species composition and biomass on the one hand and environmental variables on the other hand, was analysed in a Canonical Correspondence Analysis, for both compartments separately. The analysis revealed that the phytoplankton assemblage more and more obtained a summer character, extending its growth season both earlier and later in the year. The transition of spring to summer phytoplankton assemblages proceeded parallel to the main light-turbidity gradient. The factor light did not only explain the seasonal pattern, but also the long-term trend from pre-barrier to barrier period. Partial Detrended Correspondence Analysis after correction for the mean seasonal pattern confirmed this trend significantly.