The water samples that were used to compile this dataset were collected between August to October 1996 at exactly low tide from a jetty, about 5 m from the bank. To obtain information on the spatial distribution of phytoplankton populations, additional samples were taken along a longitudinal transect on three occasions during the sampling period. Corresponding environmental data were measured in situ (temperature, secchi depth), or after filtration and analysis of subsamples (salinity, nutrients, chlorophyll a) or was gathered from different sources e.g. Royal Belgian Meteorological Institute (Irradiance data), the Administration Waterways and Maritime Affairs (freshwater discharge). Details on the sampling and analyses procedures are described in the related publication. This dataset was compiled and used in the framework of the research that was conducted by Koenraad Muylaert, described in his Phd thesis: "Muylaert, K. (1999). Distribution and dynamics of protist communities in a freshwater tidal estuary. PhD Thesis. Universiteit Gent (RUG): Gent, Belgium. 192 pp." More specifically this dataset was used to study regulation of phytoplankton dynamics in a freshwater tidal estuary by irregular flushing events (chapter 7).