Testate amoebae are a frequently used palaeoecological proxy for reconstructing changes in palaeohydrological conditions, particularly in studies of Sphagnum-dominated peatlands. Their use in palaeoecological studies has increased following the development of transfer functions, allowing for the quantitative reconstruction of water-table depth changes through time. Increasingly, they are included in non-pollen palynomorph (NPP) studies alongside a wide range of other proxies, representing a valuable tool, particularly in multi-proxy studies.

Testate amoebae have been used for qualitative assessment of palaeohydrology in NPP studies and may aid the verification of environmental interpretations of conditions inferred from curves of NPP with unknown ecology and taxonomy. Their usefulness in such studies is limited by the destruction of tests owing to harsh chemical treatments used in pollen preparation methods. This makes community distribution data of testate amoebae derived by these methods largely unsuitable for quantitative assessment of water-table depth. Furthermore, many palynological studies combine testate amoebae as one single curve, losing further ecological detail. Patterns of change of surviving species, most commonly of Assulina, Archerella, Arcella, Hyalosphenia and Archerella flavum, remain relatively unaffected and therefore can still be useful for interpreting qualitative changes in hydrological conditions through time, particularly when coupled with other proxies.