Flood having subsided with river contained (5)
I believe the answer is:
drown
'flood' is the definition.
(thesaurus)
'subsided with river contained' is the wordplay.
'subsided with' becomes 'down' (I am not sure about the 'with' bit.**).
'river' becomes 'r'.
'contained' means one lot of letters goes inside another.
'down' enclosing 'r' is 'DROWN'.
'having' is the link.
(Other definitions for drown that I've seen before include "Become submerged" , "Sink" , "Perish in water" , "Suffocate in liquid" , "Flood (an area)" .)