Testate amoebae are a widely-used tool for palaeohydrological reconstruction from peatlands. However, it has been observed that weak idiosomic siliceous tests (WISTs) are common in uppermost peats, but very rarely found as subfossils deeper in the peat profile. This taphonomic problem has been noted widely and it has been established that WISTs disaggregate and/or dissolve in the low pH condition of ombrotrophic peatlands. Here we investigate the effect of this taphonomic problem on water-table reconstructions from thirty European peatlands through the comparison of reconstructions based on all taxa and those with WISTs removed. In almost all cases the decomposition of WISTs does not introduce discernible bias to peatland water-table reconstructions. However, some discrepancy is apparent when large abundances of Corythion-Trinema type are present (9−12 cm deviation with 50–60% abundance of this particular taxon). We recommend that WISTs should be removed before carrying out water-table reconstructions, and that the minimum count of testate amoebae per sample should exclude WISTs to ensure the development of robust reconstructions.