You have to find out the equilibrium time for your sample (by varying time interval while keeping other parameters constant). Time at which adsorption stops, that is the equilibrium time.
The questions is not clear, because it is very general. You need to know which type of media you are using, the type of equipment, and the experimental data and preliminary tests to verify flows and then be able to stablish the contact time [residence time] (related with the comment of Renu Bisht).
Water sample should an equalized sample with respect to its composition like pH etc., I mean it should be a homogenous sample. Try its treatment on a part of it. If you expect its composition is not to be homegeneous, it must be routed through an eqalization tank before any treatment.