Run into fish in Channel (6)
I believe the answer is:
trench
'run' is the definition.
The definition and answer can be both natural objects as well as being singular nouns.
Maybe there's an association between them I don't understand?
'into fish in channel' is the wordplay.
'into' indicates putting letters inside.
'fish' becomes 'tench' (tench is a kind of fish).
'in channel' becomes 'r' (I am not sure about this - if you are sure you should believe this answer much more).
'tench' enclosing 'r' is 'TRENCH'.
(Other definitions for trench that I've seen before include "Fish; move on ice" , "Cutting" , "A ditch dug by soldiers" , "Ditch, as a fortification say" , "Long, narrow excavation" .)