Tropical Storm Agnes produced a fourfold stress on the Rappahannock Estuary: first a storm tide, then river flooding and high sediment influx, followed by freshened inflow through the mouth. As flood energy dissipated through the upper estuary it broke down the normal partly-mixed regime and changed the near-bed transport direction from landward to seaward. Flooding of the lower estuary changed the partly-mixed regime to a salt-wedge and triggered a sequence of hydraulic events: (1) initial response, (2) shock, (3) rebound, (4) reversal, (5) second shock, (6) homogeneity and recovery. Net velocity and sediment transport returned to normal rates within 15 days whereas salinity recovered within 60 days. Despite high inflow, morphological changes were surprisingly small. The flood energy mainly produced a large transport of suspended sediment within the estuary. Most flood-borne sediment supplied during early flood stages was trapped landward of the fresh-salt water convergence which acted as a dynamic barrier. Sediment that escaped farther seaward in the low salinity surface layer during late flood stages was entrapped by the closed estuarine circulation which was strengthened and retained in the estuary during all stages of flooding. Of the total sediment influx, about 90% was trapped within the estuary and deposited mainly in the zone of the turbidity maximum.