Stop short of island, notwithstanding presence of flatfish (7)
I believe the answer is:
halibut
'presence of flatfish' is the definition.
'halibut' can be an answer for 'flatfish' (halibut is a kind of flatfish). I am not sure about the 'presence of' bit.
'stop short of island notwithstanding' is the wordplay.
'stop' becomes 'halt' (halt can mean to stop).
'short of' means to remove the last letter (I've seen 'shorter' mean this).
'island' becomes 'i' (geographical abbreviation).
'notwithstanding' becomes 'but' (I can't explain this - if you can you should believe this answer much more).
'halt' with its final letter taken away is 'hal'.
'hal'+'i'+'but'='HALIBUT'
Can you help me to learn more?
(Other definitions for halibut that I've seen before include "Swimmer" , "One's scaled" , "Largest flatfish" , "Large flatfish used as food" , "Large food fish" .)