Sediment with depth in a city (5)
I believe the answer is:
leeds
'city' is the definition.
(city in England)
'sediment with depth' is the wordplay.
'sediment' becomes 'lees' (lees is a kind of sediment).
'with' is an insertion indicator.
'depth' becomes 'd' (abbreviation in geometry).
'lees' placed around 'd' is 'LEEDS'.
'in a' is the link.
(Other definitions for leeds that I've seen before include "City of northern England - castle of southern England" , "Northern town" , "Yorks city" , "City near Bradford" , "English city" .)