one problem can be, that ...

one problem can be, that flood-water is getting into the well.to avoid that, you should extend the well during the dry periods to get it higher than maximum flood level and second you should seal the well outside against a drainage-impact between earth and metal-body. for that you can use expansive mortar and/or clay.

next is to search leaks in the nearer environment of the well. this could be deep roots, hedges or stakes of fences for example. to find them, often tracer-gas is used (you press it from the well outside and detect it with adequate meters.

Short version : seal the well as good as possible before it gets flooded