Missile turned over HQ, crossing river (7)
I believe the answer is:
torpedo
'missile' is the definition.
(missile from a submarine)
'turned over hq crossing river' is the wordplay.
'turned' shows that the letters should be reversed in order.
'over' becomes 'o' (cricket abbreviation).
'hq' becomes 'depot' (depot can mean a military headquarters).
'crossing' indicates putting letters inside.
'river' becomes 'r' (abbreviation for river).
'o'+'depot'='odepot'
'odepot' enclosing 'r' is 'odeprot'.
'odeprot' reversed gives 'TORPEDO'.
(Other definitions for torpedo that I've seen before include "Naval missile" , "Submarine weaponry" , "Underwater bomb" , "Destroy" , "Such as could sink" .)