Assistance please: Broken water main?

Flushed my toilet this morning and it refilled with a loud "fart" of air,
eventually followed by dirty water.

I heard on the radio scanner there's some water main and waste water repairs
down the road.

I called the water company but the gal on their end was absolutely brain dead
as to step by step procedures and wouldn't further me on to know-it-alls like
I'd hoped.

What's the sequential procedure to clear the cold and hot water pipes? I have
a septic system so I figure to drain the cold water first and the hot water
second but I can't expel all that water in a single day through a 2,000
gallon septic tank.

What would you do?

Andy