Climate change, comprising of changes in precipitation patterns, higher temperatures and sea level rises, increases the likelihood of future flooding in the Betna River basin, Bangladesh. Hydrodynamic modelling was performed to simulate the present and future water level and discharge for different scenarios using bias-corrected, downscaled data from two general circulation models. The modelling results indicated that, compared to the baseline year (2014–2015), the water level is expected to increase by 11–16% by the 2040s and 14–23% by the 2090s, and the monsoon daily maximum discharge is expected to increase by up to 13% by the 2040s and 21% by the 2090s. Sea level rise is mostly responsible for the increase in water level. The duration of water level exceedance of the established danger threshold and extreme discharge events can increase by up to half a month by the 2040s and above one month by the 2090s. The combined influence of the increased water level and discharge has the potential to cause major floods in the Betna River basin. The results of our study increase the knowledge base on climate change influence on water level and discharge at a local scale. This is valuable for water managers in flood-risk mitigation and water management.