Three examples where the Confederacy succeeded in making rivers impassable:
1. Yazoo Pass Expedition- March 11 -16th, 1863. Repeated attempts by Union gunboats to proceed down the Tallahatchie River in Mississippi were thwarted by artillery in Fort Pemberton which was located on ground between the Tallahatchie and Yazoo Rivers. The large ocean going sidewheel steamboat "Star of the West" was also sunk as an obstruction.
2. Sabine Pass, September 8, 1863. Confederate artillery in a battery located at Fort Griffin on the Texas side of the Sabine River repel a Union invasion force of 4 gunboats and 4,000 troops on transports.
3. Red River Expedition, March 10 to May 22, 1864. Certainly the land battles that accompanied this campaign receive more attention than the trials and tribulations of the Federal navy during the same period but to make a long story short...the navy turned back so the Red at some point became impassable...lets let Admiral Porter explain....
When I arrived at Springfield Landing I found a sight that made me laugh. It was the smartest thing I ever knew the rebels to do. They had gotten that huge steamer, New Falls City, across Red River, 1 mile above Loggy Bayou, 15 feet of her on shore on each side, the boat broken down in the middle, and a sand bar making below her. An invitation in large letters to attend a ball in Shreveport was kindly left stuck up by the rebels, which invitation we were never able to accept.
He goes on to say that he was preparing to remove the obstruction when he got word of Bank's retreat after the Battle of Mansfield so we will never know exactly how much more difficulty he would have had proceeding up river.
Beyond the New Falls City there was a dam, possibly another raft across the river, gun batteries at Shreveport, an ironclad, a gunboat and a ram.