The dataset contains information on total phosphorus (TP), electric conductivity (EC) of water and diatom assemblages (abundance in %) of modern sediments for 90 lakes (115 samples) of the Urals. Lake water for EC and TP was sampled several times (3-5) in the period from 2014 to 2022 in spring, summer, and autumn. We included median values of EC and TP into the dataset for transfer function development. In addition, average values, standard deviations of EC and TP, longitude, latitude and sampling depth are presented in the dataset. Diatom assemblages contain 393 species and varieties. Several lakes (15) were sampled for water and surface sediments in 2-4 points with different depth, TP, EC, or located in different parts of lake. Additional metadata contain three columns: "Species", "Authority" and "Code". Column "Species" includes names of diatom taxa. Column "Authority" contains information on authorities of taxa. Column "Code" includes diatom taxa codes in the Urals lakes dataset. For quantitative reconstruction of TP and EC with application of the Urals lakes dataset, names of diatom species in fossil record should be replaced with the appropriate codes. We developed the transfer function for quantitative reconstructions of total phosphorus ranging from 5.6 to 313 μg l-1 and electric conductivity ranging from 61 to 21.700 μS/cm. WA-PLS-Component 2 (RMSEPboot=0.2 log10 μg/l, bootstrap r2=0.6 log10 μg/l) was the best performing model for TP. WA with classical deshrinking (RMSEPboot=0.2 log10 μS/cm, bootstrap r2=0.8) was the best performing model for EC. The dataset can be independently applied for quantitative reconstructions of lake water TP and EC or joined with other diatom datasets.