Use a shop-vac to see if you can suck the hole down enough to work. There may be no trap in the rough-in, and the pipe may need to be cut to fit. If your rough in is cast iron (as it should be in Chicago), use a shielded coupler to attach a trap. If you are working with PVC, hopefully you can suck the water level down long enough to prime and cement, but you could use a shielded coupler there too if need be.
If you cannot get the water level down, you might need to dig another hole nearby to drop a trash pump into so you can try to temporarily pump down the water level around your work area.