Naturally in Lower Egypt it's seen initially (4)
I believe the answer is:
nile
'naturally in lower egypt' is the definition.
Although both the answer and definition are singular nouns, I can't see how they can define each other.
'it's seen initially' is the wordplay.
'it' becomes 'e' ('e' can mean 'electronic' which is similar to 'IT').
'seen' becomes 'nil' (I can't justify this - if you can you should give a lot more credence to this answer).
'initially' says to put letters next to each other (some letters go before others).
'e' put after 'nil' is 'NILE'.
Can you help me to learn more?
(Other definitions for nile that I've seen before include "'The longest river, blue and white (4)'" , "Long river" , "white flower?" , "River at Luxor" , "Egypt's river" .)