Magistrate’s about to arrest a ruler of the waves (3,3)
I believe the answer is:
sea god
'ruler of the waves' is the definition.
'magistrate's about to arrest a' is the wordplay.
'magistrate's' becomes 'doges' (doge is a kind of magistrate).
'about' says the letters should be written backwards.
'to arrest' means one lot of letters goes inside another.
'doges' reversed gives 'segod'.
'segod' enclosing 'a' is 'SEA-GOD'.
(Other definitions for sea god that I've seen before include "Trident was carried by one once" , "Neptune, maybe" , "Neptune or Poseidon" .)