The most common and most likely answer to this crossword clue is the 7 letter word ROOKERY
I've seen this crossword clue in The Daily Telegraph
R
O
O
K
E
R
Y
More clues leading to the result ROOKERY
- Stony garden has circle for a hundred nesting birds
- Place for birds with eggs by railway, all right for nesting
- Fine for breaking eggs, overturning younger birds’ nests
- Castle nearly losing odd bits in overcrowded area
- Where birds breed round New Yorker circles
- Colony on high fine with queen in old kingdom lacking leadership
- Castle on Eastern Railway is a bird’s nesting place
- Where birds hatch eggs, sheltering fine over railway
- Swindling Conservative wiped out bird colony
- New Yorker putting duck in home for birds
Buddy explains!

The straight part
We know that "Natural nursery" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case natural nursery = rookery.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does ROOKERY mean?
ROOKERY noun- A colony of breeding birds or other animals.
- A crowded tenement.
- A place where criminals congregate, often an area of a town or city.