I know the stretch immediately below Pagosa is called Mesa Canyon and is considered class III-. However, I have not floated it, and do not know what lies below there.
There was this quick blurb about it:
NAVAJO RIVER NORTHERN NEW MEXICO- NAVAJO LAKE STATE PARK
One such example is the 25 mile Navajo River run from Dulce New Mexico that during high water runs into Navajo
Lake and Navajo Lake State Park that only gets water when the Azotea Trans Basin Tunnel is full. It bears
scouting the entire route. The river above the lake is not administered by New Mexico State Parks.
I have only done the Pagosa to Trujillo Road run, which is about 14 miles and generally done as a day trip. It's III- as lmyers said. There is some Forest Service land in this section, but it's mostly private. Get a good map. The Utes do not allow camping on their section. I haven't done the whole float down to Navajo Reservoir, but I have fly fished the lower section wading. It's not especially aesthetic, nor particularly interesting paddling/rowing. Fishing was pretty marginal too. The Mesa Canyon section is quite pretty, and has great fishing. Here's a previous thread on this topic.
Also, the Navajo River blurb mentioned above is not the San Juan.
I've floated Mesa Canyon but its been a few years so take this with a grain of salt. Its a beautiful stretch of river but you're not going to flush your adreneline glands out on this one. I'm not sure what the river is like now that they've built a playpark but as of a few years ago, your best chance for a flip was on the one Class III- rapid of the run, immediately upstream of the hot springs (at least you'd have a good audience!). After that there are only a couple of Class II rapids once you get past town.
The put-in is in Pagosa Springs, just upstream of the bridge over the SJ River, behind a little strip mall where there's a good breakfast place. You've got to haul your boat over the bikepath and a couple of large boulders but it can be reached with a trailer if you work a little. The takeout is good for loading onto a trailer where the road comes right to river level.
If you float this section and want to camp out, make sure you have good maps showing public and private land. My understanding is that most, if not all, of Mesa Canyon is private land and that the landowner does not allow camping there and there's only one place where its legal to stop. Apparently at the behest of the outfitters that run Mesa Canyon, the landowner has been gracious enough to designate about a one-acre meadow open to boaters to stop and have lunch or take a break on his land. This rest area is on river Left about mid-way down the run and is marked by a large sign.
Have a good trip and please give us an update on the stretch after you float it.
It's very alpine, with lots of ponderosas and nice cliffs. There are a few horseshoe-shaped fish structures in the Bass Ranch section to keep an eye on, but no holes of consequence. Should be enough water this year to keep the run interesting up to early July.
I ran the Mesa Canyon section, accompanying the outfitter, in the middle 90s. There is some class 2++ in mid run. Otherwise it's scenic and pretty easy unless you look for trouble. The outfitter had us stop about mid run in a place allowed by the Ute Indian organization.
In my opinion, the upper, Mesa Canyon, section is not long enough for an overnight unless you really were to "dog" it.
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