A few questions to start with!

1) How long has the pit been flooding?
2) Does it only do it after it rains for a few days?
3) How is the pit constructed?(concrete, brick etc)
4) Are you on mains drainage?
5) Have you a leaking watermain?

IME pits always flood due to groundwater unless tanked, it's just a
question of when and how much. I'd look to waterproof the pit before I
even considered doing more than putting a rod down the drain to check if
had been tree rooted. Drains normally(even Victorian) do not have
stagnant water levels in them, the flow is pretty good provided toilet
waste is passing regularly.

Regards
Capitol