This dataset comprises multiple baseline and future ensembles of hydrological model estimates of monthly mean and annual maximum river flows (m3s-1) on a 0. 0.008333° × 0. 0.008333° grid (approximate grid of 1 km × 1 km) across Peninsular Malaysia. Specifically, these are provided for historical (1971 to 2005) and projected future (2006 to 2099) periods, for 3 Representative Concentration Pathways (RCPs). This dataset is the output from the Hydrological Modelling Framework for Malaysia, or “HMF-Malaysia” model. The projected future hydrology simulations are provided for CORDEX-SEA (Coordinated Regional Downscaling Experiment – South East Asia) three RCPs (RCP2.6, RCP4.5 and RCP8.5) assuming (i) current artificial influences (CAI) such as water transfers and diversions and (ii) planned future artificial influences (FAI). This dataset is an output from the hydrological modelling study from the Malaysia - Flood Impacts Across Scales (FIAS) project.