Lagoon site (5)
I believe the answer is:
'lagoon site' is the definition.
(I've seen this in another clue)
This is all the clue.
(Other definitions for atoll that I've seen before include "Bikini for one" , "tropical paradise?" , "Land around a lagoon, such as Bikini" , "Coral circle" , "land threatened by rising sea levels" .)