The most common and most likely answer to this crossword clue is the 12 letter word SUBTERRANEAN
S
U
B
T
E
R
R
A
N
E
A
N
Buddy explains!
The straight part
We know that "beneath the waves" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case beneath the waves = subterranean.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 SUBTERRANEAN mean?
SUBTERRANEAN adjective- Below ground, under the earth, underground