Brown river in Scottish city (6)
I believe the answer is:
dundee
'scottish city' is the definition.
(city in Scotland)
'brown river' is the wordplay.
'brown' becomes 'dun' (dun is a kind of brown).
'river' becomes 'Dee' (River Dee).
'dun'+'dee'='DUNDEE'
'in' is the link.
(Other definitions for dundee that I've seen before include "City in Scotland and a cake" , "Tayside city, Dens Park team" , "Crocodile -; - cake" , "Scots city of cake fame" , "Scottish city with cakes" .)