River enters sea by a harbour (6)
I believe the answer is:
marina
'harbour' is the definition.
(marina is a type of harbour)
'river enters sea by a' is the wordplay.
'river' becomes 'r' (abbreviation for river).
'enters' indicates putting letters inside.
'sea' becomes 'main' (synonyms).
'by' means one lot of letters go next to another.
'r' placed within 'main' is 'marin'.
'marin'+'a'='MARINA'
(Other definitions for marina that I've seen before include "Docking facility for pleasure craft" , "Base for pleasure boats" , "Docking place for pleasure craft" , "Yachting centre" , "Place for mooring boats" .)