Little is known about the century-scale response of water levels in inland estuaries to sea-level change and human modifications to estuarine morphology. This study explored the ability of using testate amoebae (Protozoa, Rhizopoda) from sediments of a freshwater tidal marsh as indicators of water level in an inland estuary. The hypothesis was that modern testate amoeba assemblages change with surface elevation (approximately the duration of tidal flooding) within a freshwater tidal marsh. Variation in testate amoeba assemblages in relation to multiple environmental variables and sediment characteristics was studied through redundancy analysis. This demonstrated that a significant part of the variation in modern testate amoeba assemblages could be explained by flooding frequency, surface elevation, organic content and particle size of the soil. Transfer functions, partial least squares and weighted average regressions were made to show that testate amoebae can be used for reconstruction of water level (with an accuracy of 0.05 Normalized Elevation). A preliminary test of application of the transfer function to palaeo testate amoeba assemblages showed promising results. Testate amoebae from a freshwater tidal marsh provide a potentially powerful new tool for estuarine water-level reconstructions. Copyright © 2011 John Wiley & Sons, Ltd.