Few studies have examined testate amoebae assemblages of estuarine tidal marshes. This study investigates the possibility of using soil testate amoebae assemblages of a brackish tidal marsh (Scheldt estuary, Belgium) as a proxy for water level changes. On the marsh surface an elevation gradient is sampled to be analyzed for testate amoebae assemblages and sediment characteristics. Further, vegetation, flooding frequency and soil conductivity have been taken into account to explain the testate amoebae species variation. The data reveal that testate amoebae are not able to establish assemblages at the brackish tidal marsh part with flooding frequencies equal to or higher than 36.5%. Further, two separate testate amoebae zones are distinguished based on cluster analysis. The lower zone’s testate amoebae species composition is influenced by the flooding frequency (~ elevation) and particle size, while the species variability in the higher zone is related to the organic content of the soil and particle size. These observations suggest that the ecological meaning of elevation shifts over its range on the brackish tidal marsh Testate amoeba assemblages in such a brackish habitat show thus a vertical zonation (RMSEP: 0.19 m) that is comparable to the vertical zonation of testate amoebae and other protists on freshwater tidal marshes and salt marshes.