This repository provides training sets and R scripts for the development of three transfer function models that allow reconstructions of Holocene hydrochemical or hydrological (hydroclimatic) conditions from testate amoeba assemblages preserved in mires of East-Central Europe. Specifically, the repository contains (i) the full dataset and an R script for the development of the final MLRC model for inferring past water-mineral richness (expressed as pH) in various types of mires; (ii) the minerotrophic subset and an R script for the development of the final WAPLS com1 model for the reconstructions of past water-mineral richness (expressed as pH) in rich and calcareous fens; and (iii) the ombrotrophic subset and an R script for the development of the final PLS com2 model for inferring past depth to the water table (DWT) in bogs and poor fens. Additionally, the repository includes the original versions of the full, minerotrophic and ombrotrophic training sets (i.e., the versions before the removal of outlier samples and rare taxa due to the optimization of the transfer function models), and the compiled dataset, from which the three above-mentioned training sets were generated. For details, see the paper by Šímová et al. (under review).