Stony garden has circle for a hundred nesting birds (7)
I believe the answer is:
rookery
'nesting birds' is the definition.
(group of birds nesting together)
I don't understand how the rest of the clue works.
(Other definitions for rookery that I've seen before include "Breeding-place of birds, penguins, seals" , "Community of birds" , "Seal, penguin, colony" , "Lofty breeding-place" , "Colony of penguins or seals" .)