Sediment management issues are of prior concern in the Danube Basin (800000 km2) for provision of navigation, flood control, energy services, and to ensure good ecological status of its aquatic habitats. This study aimed at producing a SWAT sediment model of the entire Danube Basin for assessing current sediment fluxes and for identifying potential knowledge gaps. The model set-up accounted for current adoption of conservation measures based on available pan-European datasets. The simulation period was 1995-2009, following five years of warm-up. Hydrologic Response Units (HRUs) gross erosion and sediment yields were broadly calibrated using ancillary data that comprised datasets of long term measurements in plots and small catchments (area up to 500 km2), and gross erosion rates published in national and pan-European maps. HRU mean annual sediment yields varied across land use type and with soil and water conservation management, with mean value of 280 t/km2/y. Mean annual sediment concentrations (SSC, [mg/L]) data from 269 gauging stations (2968 station-year entries) were used for calibration of in-stream sediment routing parameters. SSC residuals (simulations-observations) median in the calibration dataset was 2 mg/L (interquartile range -14; + 22 mg/L). These results were confirmed in the validation dataset on additional 172 gauging stations data (1457 station-year entries), with median residual of 9 mg/L (interquartile range -9; + 40 mg/L). Annual specific sediment yields (SSY, [t/km2/y]; 689 data-entries in 95 stations) were employed for further evaluation of model results. SSY simulations percent bias was -21.5%. No error pattern in relation to reach scale was detected. Overall, the basin-wide model performance was considered satisfactory. Sediment fluxes appeared overestimated in the Sava and Velika Morava regions, and underestimated in the Siret-Prut and Romanian Danube water management regions. Elsewhere, modelled sediment fluxes were unbiased. According to the modelled annual sediment budget, most sediments were generated in the land phase (HRU sediment yields). Streambank erosion was estimated to be important in the high stream power reaches of the Alpine region . When considering the whole basin, streambank degradation contributed about 5% of sediments. Sediment trapping in reservoirs and floodplain deposition appeared underestimated in the model and counterbalanced by high stream deposition. Knowledge gaps affecting the sediment budget were identified in the need to include other sediment processes, namely glacier erosion, gully erosion and mass movements, and to improve stream hydraulic geometry, which impacted in-stream sediment dynamics. Contemporary sediment fluxes were about one third of mean values reported for the 1980s for several tributaries of the Middle and Lower Danube. The reduction of sediment yields may be attributed to anthropic activities, such as increased sediment trapping in reservoirs, land use changes, and to a lesser extent the introduction of soil conservation practices.