This study reports on new projections of discharge to the Baltic Sea given possible realisations of future climate and uncertainties regarding these projections. A high-resolution, pan-Baltic application of the Hydrological Predictions for the Environment (HYPE) model was used to make transient simulations of discharge to the Baltic Sea for a mini-ensemble of climate projections representing two high emissions scenarios. The biases in precipitation and temperature adherent to climate models were adjusted using a Distribution Based Scaling (DBS) approach. As well as the climate projection uncertainty, this study considers uncertainties in the bias-correction and hydrological modelling. While the results indicate that the cumulative discharge to the Baltic Sea for 2071 to 2100, as compared to 1971 to 2000, is likely to increase, the uncertainties quantified from the hydrological model and the bias-correction method show that even with a state-of-the-art methodology, the combined uncertainties from the climate model, bias-correction and impact model make it difficult to draw conclusions about the magnitude of change. It is therefore urged that as well as climate model and scenario uncertainty, the uncertainties in the bias-correction methodology and the impact model are also taken into account when conducting climate change impact studies.