Based on hydrological data observed at Lijin gauging station from 1950 to 2008, the temporal changes of water discharge and sediment load of the Yellow River into the sea were analyzed by the wavelet analysis, and their impacts on the estuary were investigated in different periods based on the measured coastline and bathymetry data. The results show that: (1) there were three significant periodicities, i.e. annual (0.5—1.0-year), inter-annual (3.0–6.5-year) and decadal (10.1–14.2-year), in the variations of water discharge and sediment load into the sea, which might be related to the periodic variations of El Nino and Southern Oscillation at long-term timescales. Variations of water discharge and sediment load were varying in various timescales, and their periodic variations were not significant during the 1970s–2000s due to strong human disturbances. (2) The long-term variation of water discharge and sediment load into the sea has shown a stepwise decrease since the 1950s due to the combined influences of human activities and precipitation decrease in the Yellow River Basin, and the human activities were the main cause for the decrease of water discharge and sediment load. (3) The water discharge and sediment load into the sea greatly influenced the evolution of the Yellow River Estuary, especially the stretch rate of coastline and the deposition rate of the sub-aqueous topography off the estuary which deposited since 1976.