I think the typical run through the park begins on Cedar Creek and then goes out to 601 on the Congaree. The Paddling South Carolina book shows the last Congaree put-in before the park off Old State Rd., 45 miles from 601. It would be an adventure!

You can put in at the END of the Congaree Creek trail which is also off bluff road, but several miles past the park entrance..it will take off the 2 - 3 hours it would take to paddle all the way through. Not sure how far it is from there to the river though.

I went down this a couple of weeks ago. Here's my take on it.

Before you go, if you'll be camping you need a permit from the ranger station. Check the mosquito meter; it said moderate when I left, and that was fine. Along with the permit get their map (Congaree National Park Trail Guide) because its the best one there is of this route. It's also at
http://www.nps.gov/cong/planyourvisit/upload/cong_trailguide.pdf
Also check the water level at Gadsen station, at
http://waterdata.usgs.gov/nwis/uv?02169672
When I left there was a little over three feet of water. Below three feet, I wouldn't go.

There's two put-ins within the park. Both require lugging your boat about 50 yards along a trail. (or wheeling it on a dolly, like me :-)
I put in at Bannister's bridge, which is on old bluff road west of the ranger station. It's not much of a bridge, just a concrete overpass really. Look for a little sign marking the parking lot.

With water at three feet, I had to drag over logs five times before coming to Cedar Creek canoe launch, only two bad ones were between the wooden bridges near the ranger station. Not counting fooling around this stretch took about five hours.

Cedar Creek Canoe Launch is on south cedar creek road. Same setup there; gravel road, blocked off by a pipe gate, isolated parking lot for cars, 50 (?) yards of trail to water. Past this launch, no access till the bridge on Hwy 601. It's an overnight trip (even though I took three days), easy to camp anywhere along the way (no fires). Downstream from the Canoe Launch I dragged over just four logs. For people who don't “waste time” like I do, I'd estimate about 11 hours of canoeing. Spend the night down around Mazerk's Cut and it should work out nicely.

After leaving the CC canoe launch, you'll come to a branch off to the right: this is Horsepen Cut. There is a marker there, high up on a cypress tree, consisting of three white metal diamond shaped signs in a vertical row, reading “canoe trail” and 70, 100, and 150 respectively from top to bottom. I don't know what that refers to, but it's nice to know where you are. Horsepen Cut seemed to be all blocked up—ignore it. Keep going and before too long you'll come to a T. This is Mazerk's Cut. Go right and out to the Congaree river. You'll go fast then, there's one ginormous sand bar on the right a little before the end: play on this. Then you'll go under a railroad bridge and then Hwy 601, which has both a dock, and a beach you can come out on.

It's 15 miles of road between the 601 takeout and the Cedar Creek canoe launch. Three more miles along Old Bluff road to Bannister's bridge put-in. From B Bridge I think it's 17 miles back to I-77, Bluff Road exit.