A waterway initially remains flooded (5)
I believe the answer is:
awash
'flooded' is the definition.
('awash' can be a synonym of 'flooded')
'a waterway initially remains' is the wordplay.
'initially' indicates taking the first letters.
'remains' becomes 'ash' (I've seen this before).
The first letter of 'waterway' is 'w'.
'a'+'w'+'ash'='AWASH'
(Other definitions for awash that I've seen before include "not quite under" , "Covered by water - sounds cleansing" , "Flooded with water" , "Doused in water" , "Level with the water surface" .)