The Union fleet was not able to stop all passage of the Mississippi River. That was not their intent. But the occupation of the east and west banks of the River and the boat and cavalry patrols along with that effectively hindered the passage of large groups of troops such as regiments and large amounts of supplies and War goods such as the cattle from Texas that were needed by the east. Without the use of steamboats to cross the Mississippi the Confederate communicates with the Trans Mississippi had to be handled by what could be secreted across the river by small rafts, flatboats, barges and canoes.
The account of M.M. Parson's Missouri Brigade recrossing the Mississppi to the Trans Mississippi department, in late August 1862, and avoiding the Union patroling Gunboats is the last account that I can find of any large transportaion of a brigade sized unit with all of it supporting wagons and artillery and additional war supplies, (25 piece of additional field artillery for the Trans Mississippi) crossing the Mississippi river (from east to west, or for that matter from either direction) at any place other than at Vicksburg/Port Hudson.
That was one of the lessor points of discussion about the lost of Arkansas Post was it's loss as a safe haven for Steamboats for blockade running purposes. And one of the main reasons that gunboats like the USS Conestoga and USS Gen Bragg were assigned to patrol the mouth of the Arkansas and White Rivers into the Mississippi after the fall of Arkansas Post.