Fungal infection beginning to weaken otter at sea (3,3)
I believe the answer is:
wet rot
'fungal infection' is the definition.
(type of fungal infection)
'beginning to weaken otter at sea' is the wordplay.
'beginning to' indicates taking the first letters.
'at sea' indicates an anagram.
The first letter of 'weaken' is 'w'.
'otter' with letters rearranged gives 'etrot'.
'w'+'etrot'='WET ROT'
(Other definitions for wet rot that I've seen before include "type of decay" , "Timber fungus" .)