The main objective of this study was to project changes in the evolution of drought characteristics (frequency, duration and magnitude) during the 21st century in lowlands, highlands and mountainous regions in the Czech Republic (CR). We focused on the multi‐scalar nature of droughts as a function of the variables that govern the balance of moisture during climate change, such as precipitation, which supplies moisture, and temperature, which modulates evapotranspiration. Thereby, this issue is addressed with two drought indices, i.e. the standardized precipitation evapotranspiration index (SPEI) and the standardized precipitation index (SPI), for various lags (1, 3, 6, 12 and 24 months). To assess the impact of climate change on drought characteristics, a set of eight regional climate models (RCMs) simulations were selected for further analysis driven by five different global circulation models (GCMs) carried out in the frame of Euro‐CORDEX. Future drought changes were developed for the two representative concentration scenarios (RCP4.5 and RCP8.5). For the temporal evolution of the droughts, the monthly drought indices were calculated over the entire study period from 1961 to 2100. The SPEI showed a higher frequency in the categories of severe droughts and extreme droughts than the SPI, while the SPEI yielded fewer events in the extreme wet categories. The probability distribution of the SPEI‐6 under the RCP8.5 scenario shifted more than one and a half standard deviations in lowlands at the end of the century, peaking at −1.65 (with a probability of 10.5%). This meant that severe droughts, according to the current climate criteria, will become the new norm in the period 2071–2100.