Abstract. The main objective of the paper is to understand the contributions to the uncertainty in low-flow projections resulting from hydrological model uncertainty and climate projection uncertainty. Model uncertainty is quantified by different parameterisations of a conceptual semi-distributed hydrologic model (TUWmodel) using 11 objective functions in three different decades (1976–1986, 1987–1997, 1998–2008), which allows for disentangling the effect of the objective function-related uncertainty and temporal stability of model parameters. Climate projection uncertainty is quantified by four future climate scenarios (ECHAM5-A1B, A2, B1 and HADCM3-A1B) using a delta change approach. The approach is tested for 262 basins in Austria. The results indicate that the seasonality of the low-flow regime is an important factor affecting the performance of model calibration in the reference period and the uncertainty of Q95 low-flow projections in the future period. In Austria, the range of simulated Q95 in the reference period is larger in basins with a summer low-flow regime than in basins with a winter low-flow regime. The accuracy of simulated Q95 may result in a range of up to 60 % depending on the decade used for calibration. The low-flow projections of Q95 show an increase of low flows in the Alps, typically in the range of 10–30 % and a decrease in the south-eastern part of Austria mostly in the range −5 to −20 % for the climate change projected for the future period 2021–2050, relative the reference period 1978–2007. The change in seasonality varies between scenarios, but there is a tendency for earlier low flows in the northern Alps and later low flows in eastern Austria. The total uncertainty of Q95 projections is the largest in basins with a winter low-flow regime and, in some basins the range of Q95 projections exceeds 60 %. In basins with summer low flows, the total uncertainty is mostly less than 20 %. The ANOVA assessment of the relative contribution of the three main variance components (i.e. climate scenario, decade used for model calibration and calibration variant representing different objective function) to the low-flow projection uncertainty shows that in basins with summer low flows climate scenarios contribute more than 75 % to the total projection uncertainty. In basins with a winter low-flow regime, the median contribution of climate scenario, decade and objective function is 29, 13 and 13 %, respectively. The implications of the uncertainties identified in this paper for water resource management are discussed.