You are not supplying enough information to assist you properly.
Once you give good detailed info, one can tell you if you need protection or just diode isolation without any timers and a source active when is operational and if both working, both feeding power to the bank.
Do you have a turbine and a generator and if so, define the head, from intake to turbine, and the water volume the hydro works with, also the power generated.
Your information, though quite limited, seems to indicate that you really need change in thought to attain the best system.
A charge controller may be needed as the best arrangement for you to keep the battery full in your absence -- even charging the batteries when you are not there.
If the irrigation ditch dries is because the user is up and above you, taking the water and not below you.
Nando