The most common and most likely answer to this crossword clue is the 9 letter word COFFERDAM
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The straight part
We know that "Separate enclosure" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case separate enclosure = cofferdam.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 COFFERDAM mean?
COFFERDAM noun- A temporary watertight structure that is pumped dry to enclose an area underwater and allow construction work on a ship, bridge, or rig to be carried out; a caisson.
- An empty space that acts as a protective barrier between two floors or bulkheads on a ship.