Single rodent seen in river that's clear (9)
I believe the answer is:
exonerate
'clear' is the definition.
(synonyms)
'single rodent seen in river' is the wordplay.
'single' becomes 'one' (similar in meaning).
'rodent' becomes 'rat' (rat is a kind of rodent).
'seen in' means one lot of letters goes inside another.
'river' becomes 'exe' (River Exe).
'one'+'rat'='onerat'
'onerat' put within 'exe' is 'EXONERATE'.
'that's' is the link.
(Other definitions for exonerate that I've seen before include "Free from obligation, blame" , "Acquit" , "Justify" , "Excuse" , "Pronounce not guilty of a crime" .)