The most common and most likely answer to this crossword clue is the 6 letter word SUNKEN
I've seen this crossword clue in The Times
S
U
N
K
E
N
More clues leading to the result SUNKEN
Buddy explains!

The straight part
We know that "under the water" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case under the water = sunken.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 SUNKEN mean?
SUNKEN verb- (heading, physical) To move or be moved into something.
- (heading, social) To diminish or be diminished.
- To conceal and appropriate.
- To keep out of sight; to suppress; to ignore.
- To pay absolutely.
- To reduce or extinguish by payment.
- To be overwhelmed or depressed; to fail in strength.
- To decrease in volume, as a river; to subside; to become diminished in volume or in apparent height.
- Caused, by natural or unnatural means, to be depressed (lower than the surrounding area) or submerged
- (of eyes or cheeks) Seeming to have fallen deeper back into the face due to tiredness, illness, or old age.