Drift boats for fishing are popular for a Class I/II sixteen mile run on the San Juan River from access points below dam through the state park to Blanco most of the year. Put in for drift boat use is for fishing only below the dam. Other paddle craft only activities are prohibited by regulation.
However, you can canoe or kayak on this stretch of the river as long as fishing also takes place. Just carry your rod and reel and fishing permit and always wear a life jacket. A short trip I did was below the dam in the early afternoon and ran to Cottonwood Campground stayed overnight you can then continue on the rest of the trip the next day.
(FYI Beyond the Navajo Lake State Park to Blanco River Run section, the Blanco to Shiprock San Juan River section has two diversion dams that must be portaged. From Shiprock to Four Corners, the San Juan river is calm except for some sand waves in higher water, taking boaters past sandstone bluffs and badlands into Utah. Once into Utah, one can make a multi-day trip all the way to the Colorado River, passing such historical areas like Bluff and Mexican Hat. The river low conditions for that stretch is below 800 cfs. Very high conditions beyond Bluff can reach 6,000 cfs.)
Note: The river channel in the Park has changed.
A one-quarter mile stretch of the San Juan River below Navajo Dam has a new look since boulders were placed in the river to improve trout fishing. This is also will make some runs in the channel different for drift boats as well.
San Juan River Conditions:
San Juan River Run below Dam (Stream gage data for Below SR 173 at Archuleta, NM)