Empty discharge channel to create dock (6)
I believe the answer is:
deduct
'dock' is the definition.
(as in docking an employee's pay)
'empty discharge channel' is the wordplay.
'empty' says to hollow out the word (remove centre letters).
'channel' becomes 'duct' (synonyms).
'discharge' with its middle taken out is 'de'.
'de'+'duct'='DEDUCT'
'to create' acts as a link.
(Other definitions for deduct that I've seen before include "Make a subtraction" , "Withhold" , "Remove" , "Subtract, take away" , "Knock off" .)