Scottish island in which a river flowed (5)
I believe the answer is:
arran
'scottish island' is the definition.
(island off the coast of Scotland)
'a river flowed' is the wordplay.
'river' becomes 'r' (abbreviation for river).
'flowed' becomes 'ran' ('run' can be a synonym of 'flow').
'a'+'r'+'ran'='ARRAN'
'in which' is the link.
(Other definitions for arran that I've seen before include "Firth of Clyde island" , "Isle near Firth of Clyde" , "Scottish island" , "Scottish territory" .)