Numerous palaeoecological studies have used testate amoeba analysis to reconstruct Holocene hydrological change in peatlands, and thereby past climatic change. Current studies have been almost exclusively restricted to ombrotrophic bogs and the period since the fen–bog transition. Although the critical link between peatland surface wetness and climate is less direct in minerotrophic peatlands, such records may still be of value where there are few others, particularly if multiple records can be derived and inter-compared. Expanding the temporal and spatial scope of testate amoeba-based palaeohydrology to minerotrophic peatlands requires studies to establish the primacy of hydrology and the efficacy of transfer functions across a range of sites. This study analyses testate amoeba data from wetlands spanning the trophic gradient in the eastern Mediterranean region. Results demonstrate that different types of wetlands have distinctly different amoeba communities, but hydrology remains the most important environmental control (despite water table depth being measured at different times for different sites). Interestingly, Zn and Fe emerge as significant environmental variables in a subset of sites with geochemical data. Testate amoeba–hydrology transfer functions perform well in cross-validation but frequently perform poorly when applied to other sites, particularly with sites of a different nutrient status. It may be valid to use testate amoebae to reconstruct hydrological change from minerotrophic peatlands with an applicable transfer function; however, it may not be appropriate to use testate amoebae to reconstruct hydrological change through periods of ecosystem evolution, particularly the fen–bog transition. In practice, the preservation of amoeba shells is likely to be a key problem for palaeoecological reconstruction from fens. Copyright © 2010 John Wiley & Sons, Ltd.