Changes in low flow indices under future climates are estimated for eight catchments in Poland. A simulation approach is used to derive daily flows under changing climatic conditions, following RCP 4.5 and RCP 8.5 emission scenarios. The HBV rainfall–runoff model is used to simulate low flows. The model is calibrated and validated using streamflow observations from periods 1971–2000 and 2001–2010. Two objective functions are used for calibration: Nash–Sutcliffe and log transformed Nash–Sutcliffe. Finally, the models are run using the bias-corrected precipitation and temperature data simulated by GCM/RCM models for the periods 2021–2050 and 2071–2100. We estimate low flow indices for the simulated time series, including annual minima of 7-day mean river flows and number, severity and duration of low flow events. We quantify the biases of low flow indices by N-way analysis of variance (ANOVA) analysis and Tukey test. Results indicate a large effect of climate models, as well as objective functions, on the low flow indices obtained. A comparison of indices from the two future periods with the reference period 1971–2000 confirms the trends obtained in previous studies, in the form of a projected decrease in the frequency and intensity of low flow events.