By holding water, is shown to be intelligent (6)
I believe the answer is:
brainy
'to be intelligent' is the definition.
(similar in meaning)
'by holding water' is the wordplay.
'holding' indicates putting letters inside.
'water' becomes 'rain' (rain is a kind of water).
'by' going around 'rain' is 'BRAINY'.
'is shown' acts as a link.
This may not be right. Some or all of it may belong to another bit of the clue.
Can you help me to learn more?
(Other definitions for brainy that I've seen before include "Clever, got lots of grey matter" , "Intellectual" , "Binary (anag.)" , "Highly intelligent" , "Showing intelligence" .)