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The head of navigation of the Mississippi River depends on the type of craft and on the source you look at. For large oceangoing ships, it seems to be Baton Rouge, but otherwise, seems to be the Coon Rapids Dam in Coon Rapids, Minnesota, or perhaps Minneapolis-St. Paul, which is quite close by. According to Wikipedia, that's about 850 miles.

In a 40-foot schooner with oars rather than motor as the secondary propulsion, how long would it take to sail that distance upriver?

(This is for a story set in preindustrial times, hence no motor. According to Wikipedia, before the Coon Rapids Dam was built in 1913, steamboats could occasionally go upstream as far as Saint Cloud, Minnesota, depending on river conditions, but that's not a big difference. At any rate, I'm not concerned about bridges and dams as obstacles, but about considerations like river width and current.)

According to the answers to Is the head of navigation same for sailing and motorboats? the head of navigation for a sailing boat can be somewhat more restrictive than a motor boat, because of the need for a deeper keel. But for a river the size of the Mississippi, it should still be most of the way up?

I'm pretty sure it's not correct to just divide the distance by the average speed of a sailing boat. For one thing, the current will be against you all the way. For another, the number of days on which you can productively sail, might be less on a river, if having to stay within the confines of the river, restricts tacking? But that might not be a consideration on a wide river like the Mississippi? But it might become one as the river narrows as you go upstream?

If it makes a difference, the trip would take place in June. I think that's a positive, from the perspective of spring/summer rain/snowmelt making the river deeper?

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It's going to be slow, with a lot of rowing.

Looking at the prevailing winds, to get an estimate of how much the wind will be on your side, it's not good news. In June, at Greenville Airport the wind is more likely to be against you than on your side, as you head broadly north upstream. This is true for the majority of reporting stations on the prevailing winds map. It's going to be slow.

The river is wide enough to tack in most places at least as far as Davenport. Tacking when the current is against you as well as the wind will be very slow as tacking relies on the water resisting downwind motion, but if the flow is going that way anyway, you'll drift downstream. A schooner can (according to this reddit thread) get to somewhere between 45°and 60° to the wind. That's pretty good. Tacking will also be complicated by the nature of the channel - lots of shallows, and even in places a braided flow with many islands. There's going to be a lot of rowing. As the river gets narrower, more time will be lost to the more frequent turns.

Why did Lewis and Clark use square rigged boats? discusses river sailing at roughly the right time. They were on smaller rivers than the lower reaches of the Mississippi, but their boats were optimised for human power with sailing secondary, so didn't have much of a keel. (I found a source saying they were under sail something like 10% of the time). Leeboards would help by acting as a keel when tacking but not getting in the way when it got shallow.

The course of the river has changed a lot since then - generally it's been straightened, so they would have had further to go, but the straightening will have increased the flow so modern navigators would have to work against more current.

Snowmelt will make it deeper, but will also make it flow faster, so more current to work against. You can get further but more slowly.

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