Central Chile has been affected by a sustained deficit in precipitation since 2010, the so-called mega drought, that has led to decreased water discharge in the fluvial basins of this region, affecting sediment fluxes. We investigate changes in sediment fluxes in the Itata River Basin (36-37°S, 11,326 km2) in central Chile over a period of 30 years (1986–2017) to evaluate the role of the mega drought in this region. We use a dataset of water discharge and suspended sediment concentration measured on a daily basis from a network of gauging stations that cover the basin from the mountain area to the river mouth. We estimated temporal variations in sediment fluxes within the basin. When comparing the pre-drought (1986–2009) and drought (2010–2017) periods, we found that annual sediment fluxes during the mega drought decreased between 28% and 67% from pre-drought values with variable intensity among the main tributaries. In addition, the season of maximum sediment transport in the basin has shifted from May–June to August during the mega drought along with a shift in the seasonality of maximum water discharge. We interpret that the precipitation deficit during the mega drought delays the recharge of the soil moisture and the establishment of favorable conditions to mobilize sediment in hillslopes. Because sediment transport in the basin occurs under conditions of lower water discharge compared to the pre-drought period, we also interpret the drought inhibits sediment transport in this system. Considering future climate projections for central Chile, it is likely that sedimentary dynamics in this basin, as well as similar fluvial basins in the region, will continue changing as the dry hydroclimatic conditions continue in the coming decades.