Hi Sumit,
To apply a varying water level as downstream boundary condition, you need to:
1: create a time series containing the water level data. Simply create a new time series file, and then paste your data into this file.
2: in MIKE 11, open the boundary file, and add a boundary condition at the downstream end of your model, where you want to apply the water level data. Select the boundary type "Water level", and in the lower table, select your time series.
Hope this will help.
Regards,
Mathieu