Is datum line necessary for the analysis of depth water table fluctuation or the average line of whole command can be take as datum line?

The water which rises to the root zone depth of the crops such that salts accumolates in the root zone of the crops which retards its growth. The water table should be lowered to such a depth well below the root zone and well below not to rise as capillary water to the root zone. For a specific area under consideration the depth of water table is taken in several points to that to consider a base line and direction of flow of water to drain away this excess water.

1-Sudden closure and opening of the valves.2-sudden closing and opening of the pumps

There is no hard and fast rule to fix up the datum. It is question of convenience and convention. You may take datum where ever you feel like, fixing it for your convenience in a particular  case study analysis. The only point of concern is that it must be same for the entire problem you are taking consideration of. It simply gives you the frame of reference from where variables such as water table, hydraulic line etc are computed ..rest fluctuation etc are relative to datum....:-)

Mr. Khalil,  my Q is about the analysis and the datum line for taking as a reference for water table levels.

well, your answer is also useful, but it is for the purpose of drainage.

I echo with Mr. Khalil to drain away the excess water.