Dataset contains data on phytoplankton that was sampled in riverine stations, in brackish stations and in freshwater tidal estuarine stations of the basins of the Scheldt estuary. Subsurface samples (0,5m depth) were taken in the estuary and its tributaries in summer (22-25 August 1995, 21 samples) and spring (11 April 1996, 11 samples). Both unconcentrated (for quantitative cell counts) and net (mesh size 10 mm) samples were taken. All phytoplankton taxa were identified and phytoplankton biomass was determined. Results were related to some important abiotic variables. Conductivity (measured with a WTW LF91), dissolved oxygen concentration (measured with a WTW oxi 61) and Secchi depth (measured by means of a black and white disc of 0.25 m diameter) were recorded at each sampling station. Samples for nutrient analysis (nitrate, ammonia and phosphate) were stored frozen and analyzed later with a Skalar (type AII flow system) autoanalyser. River discharge data for Schelde and tributaries were obtained from Administration for Waterways and Maritime affairs. 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 the structural characteristics of phytoplankton assemblages in tidal and non-tidal freshwater systems (a case-study from the Schelde basin). (chapter 6).