The Mississippi is not a difficult river and suitable even for beginners. Still each river section has its specific problems you should take into consideration:
Extricating my boots from the mud
Upper Mississippi to Minneapolis: Due to the record low water levels we encountered tons of class 1 rapids in this section - not the greatest situation for foldable kayaks. Brian poked holes in his boat already on day 2 and the situation became so bad that we hitched around two especially bad spots. In a normal water year this should not be much of a problem though. Lake Winnie poses another problem: It is huge and the wind can create waves so high that even motorized fisher boats capsize. Each year people die on Lake Winnie, so only attempt it in good weather conditions and stay close to the shore. The DNR maps recommend "portaging" around it, but there is no commercial shuttle service to help you. We were just incredibly lucky to run into Richard, a local who invited us to stay in his back yard and ended up taking pity on us. The DNR campsites are nice, but a bit of an annoyance. Due to erosion they are usually situated high up on a river bank with no beaching area and an incredibly slippery slope to climb up. For me they were not worth the effort and I much preferred easier free camping spots. Another problem that is probably due to the low water is mud. When we beaching we got sometimes stuck in mud really badly - we could only get unstuck with the help of pieces of wood to step on.
Getting out of the lock
Minneapolis to St. Louis: Locks are the biggest problem in this section. With a tail wind the area between the lock walls where you have to pull the lock cord can become a choppy nightmare. Bring a cell phone and lock phone numbers so that you can inform the lock master when it gets too dangerous to paddle inside. Getting out of the lock can be equally choppy if the adjacent dam releases water. But as soon as you have passed the lock walls the water will calm down - you just have to survive a couple of hundred metres by paddling fast and furiously.
Getting stuck behind a barge at a lock is a major annoyance - but there is nothing you can do about as commercial barge y traffic has priority. A double barge had to be taken apart to be locked through and this process takes two hours. Never pass a barge waiting in front of a lock. Use your cell phone to call the lock master and ask for instructions. Skippers and lock masters are usually very friendly to paddlers you might be squeezed in before a barge - but always ask for instructions first, don't try to jump the line on your own.
A barge from behind
Lower Mississippi: Increased barge traffic is the biggest problem here. The river is wide and you always want to be on the correct side when passing a barge - and that means crossing the shipping channel often. This sounds easy but can be a problem. These huge barges cannot pass each other in bends and therefore the upstream barge waits for a downstream barge before the bend. Sometimes several barges pile up waiting and once they start moving you cannot pass between them - you are stuck. Also keep in mind that these barges take a lot of room to turn. Luckily everything moves very slowly and you'll have plenty of time to figure out what to do. The barges have loudspeakers and if you do something stupid you might get yelled at. Tug boats are much more difficult to predict. They move faster and cross the shipping channel back and forth. Luckily you'll only encounter them around big cities and industries.