Predicting the success of future investments in coastal and estuarine ecosystem restorations is limited by scarce data quantifying sediment budgets and transport processes of prior restorations. This study provides detailed analyses of the hydrodynamics and sediment fluxes of a recently restored U.S. Pacific Northwest estuary, a 61 ha former agricultural area near the mouth of the Stillaguamish River in Washington, USA. Water level, flow velocity, and suspended-sediment concentration (SSC) were measured between 21 March 2014 and 1 June 2015 at breaches excavated in the former flood-protection levee to determine transport patterns and the net sediment budget of the restoration area. SSC within the restoration area was primarily controlled by SSC variability of the nearby main stem Stillaguamish, but coastal processes also played a major role in sediment delivery. Fluvial sediment loading was dominated by runoff events associated with rainfall that lasted hours to a few days. Additionally, the 22 March 2014 SR 530 (Oso) landslide elevated sediment supply to the restoration area and coastal region for several weeks, indicating the importance of distal geomorphic events to coastal sediment budgets in small mountainous river systems. Sediment fluxes were controlled by river SSC and tidal dynamics, which set the quantity of water transported into the restoration area. Peak water discharge at the restoration area was about 12% of the river discharge, and peak sediment flux at the restoration area was about 5% of the river sediment discharge, although net sediment import was <1% of the total river load. Although sediment was imported to the restoration area, and inferred rates of accretion appear sufficient to keep pace with present rates of local sea-level rise, full recovery is challenged by significant lost grade from historical subsidence and will likely take decades to centuries. These results have implications for estuary restoration planning globally and indicate the importance of understanding coupled fluvial–coastal processes.