River freshwater fluxes are fundamental inputs for regional and global ocean models. Nonetheless, most models are currently forced by climatological runoff data, encompassing several limitations and resulting in significant biases in the simulated ocean conditions. This study evaluates daily river discharge into South East Asia (SEA), a region having one of the greatest runoffs in the world. The discharge data are provided at 1/10° resolution by the Global Flood Awareness System (GloFAS) reanalysis through comparison with observed river discharge records and climatology. The advantages of using such a high resolution runoff product in a regional numerical ocean simulation are assessed by looking at its impact on the variability and distribution of the simulated sea surface salinity (SSS), mesoscale processes and particles’ Lagrangian dispersion within the Indonesian seas. Our results show a satisfying performance of the GloFAS product for the major rivers of the South China Sea, while no systematic errors were identified in the remaining areas of interest. Finally, for a realistic modeling of the whole SEA region, we underline the importance of using accurate river discharges in order to properly reproduce the local mesoscale dynamics, which play a key role in shaping the SSS patterns and affect the surface stranding of marine debris.