Ship from Portugal at back of queue entering waterway (9)
I believe the answer is:
privateer
'ship' is the definition.
(privateer is a kind of ship)
'portugal at back of queue entering waterway' is the wordplay.
'portugal' becomes 'p' (common abbreviation eg on car number plates).
'back of' suggests the final letters.
'entering' indicates putting letters inside.
'waterway' becomes 'river' (I've seen this before).
The final letter of 'queue' is 'e'.
'at'+'e'='ate'
'ate' going into 'river' is 'rivateer'.
'p'+'rivateer'='PRIVATEER'
'from' acts as a link.
(Other definitions for privateer that I've seen before include "Sailor may go on it" , "Drake, for example" , "Privately-owned warship" , "Government-commissioned vessel authorised to prey on enemy shipping" , "Armed ship used in war but not government-owned" .)