Body of water in the past flooding half the capital (6)
I believe the answer is:
lagoon
'body of water' is the definition.
(lagoon is a kind of body of water)
'past flooding half the capital' is the wordplay.
I cannot really see how this works, but
'past' could be 'ago' ('ago' can be similar in meaning to 'past') and 'ago' is found in the answer.
This may be the basis of clue (or it may be nonsense).
'in the' acts as a link.
(Other definitions for lagoon that I've seen before include "Area inside atoll" , "Atoll's enclosed water" , "Salt water lake surrounded by reef or sand" , "A salt-water lake enclosed by reef" , "A salt-water lake in the sea" .)