Passage which crosses river, ending in Idaho (6)
I believe the answer is:
throat
'passage' is the definition.
(throat is a kind of passage)
'which crosses river ending in idaho' is the wordplay.
'which' becomes 'that'.
'crosses' means one lot of letters goes inside another.
'river' becomes 'r'.
'ending in' suggests the final letters.
The last letter of 'idaho' is 'o'.
'r'+'o'='ro'
'that' enclosing 'ro' is 'THROAT'.
(Other definitions for throat that I've seen before include "It's inside the neck" , "Passage to the stomach and lungs" , "Gorge - frog's location?" , "Hot rat (anag) - body part" , "end of gaff" .)