Besides beaver dams, between Itasca and the Twin Cities there are probably not more than about a dozen places where portaging is required. Most of them are around dams, but occasionally you'll encounter a culvert going under a road which doesn't have enough space to float through. I can only remember one place, in my first day out from Lake Itasca, where there was a small stretch of rapids going over what appeared to be an old dam or bridge, that required a portage. Between St. Paul and the Gulf, the Chain of Rocks, near St. Louis, is the only place that might require a portage. I did portage over the spillway at a lock and dam a couple of times to avoid a long wait for the lock.
A person in a small boat or canoe has both advantages and disadvantages with regard to towboats. First, towboats have to stay in the navigable channel, which makes it easy, most of the time, to stay out of their way. Secondly, they are loud—often you can hear them coming before you see them. On the other hand, you have to assume that they can't see you. Occasionally, when I was trying to take advantage of a strong current, I would find myself in the channel when a towboat would appear from around the corner. At least twice I had no choice but to pass within a few yards of one between it and the river bank. It is a sobering experience. An interesting thing I found out from one towboat captain is that news of my presence was being passed up and down the river between the towboats via their radios. I was either famous or a notorious fool!
There are, however, things that can be done to avoid some of the wind. The most important one is to get on the river early, before the wind comes up, particularly if you're starting out with a big pool or open area to cross. Secondly, whenever possible, stay along the lee bank. Neither of these will get you out of the wind completely, but they should help.
Down the length of the Mississippi valley there are numerous other weather hazards—thunderstorms, hail, tornadoes—a weather radio could come in handy to help avoid these. The time of year you choose to make your trip can also make a difference, but there are other factors to take into consideration when planning when to go that might be more important. Given the size of the Mississippi and the amount of time you'll be spending on it, there is no way to avoid some severe weather. Being prepared with the right equipment and using common sense are probably the best two suggestions I can give.
Water was somewhat a different story. With the special food, I could wait until I came to an easily accessible town and stop. Water could not wait. In the Headwaters area I carried a Swiss-made Katadyne filter and drank filtered river water. Once I passed below the Twin Cities, however, I felt I couldn't trust even filtered water (due to chemical pollutants that might be present), so I carried a collapsible 5-gallon water container which I refilled at every opportunity. In the course of the trip there was only one time when I ran short of water and had to ration for a day or two.
The other insect to worry about is the deer tick, which can cause Lyme disease.
Mississippi River Resource Page
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