Le means the, so it refers to a specific bank account, usually one already known from the context.
Possible alternatives:
So le is not a grammar rule specific to this phrase; it just depends on what account you are talking about.
A careful pronunciation is approximately:
Le compte bancaire est à découvert
luh kont ban-kair ay-ta day-koo-vair
A few useful notes:
So in connected speech, the middle often sounds smooth: bancaire est à.