Here's a little history about the San Juan River.
The San Juan River is a tail water fishery below the Navajo Dam outside of Farmington NM. Navajo Dam is located in the northwest corner of NM about seven miles from the Colorado border. The river flows from New Mexico touches Colorado and into Utah. 
The dam is stone and earth, no concrete. The dam was completed in 1962 for flood control. Once the dam was completed and the Navajo Reservoir filled with water, the quality of downstream water changed. The release water temperatures were considerable cooler since the water released was farther and farther from the warm surface of the lake. This changed the aquatic life of the river and allowed large number of fish to grow to exceptional lengths in a short period of time. The river was stocked with Rainbows in 1960, German Browns in 1964 and later with Snake River Cutthroats in 1978. You can fish this river all year around and the water below the dam stays at a temperature between 42 and 46 degrees year around. Seasons do not affect the river so the water is always cold. Because of the water temperature and the large volume of food flowing down the growth rate of the fish is phenomenal. The fish on average range from 16 to 26 inches and three to nine pounds. This is one of the reasons that I like to venture to the San Juan as much as I can. The drive is 5 hours and 10 minutes from my house in Alpine, AZ to the river. My husband and I fish below the dam in the tail waters most of the time. Even though the fish are big, they estimate approximate 30,000 fish every quarter mile and in abundance, they are not easy to catch. The first 3 miles below the dam is a catch and release only. I think because you have to work for the fish is the reason that the river keeps drawing me back. I have hired a wading guide in the past to teach me to fish the river; what flies to use and how to read the drifts. The money and time was well spent since I catch a lot more fish these days.
You fish the river with a floating line, point fly, dropper fly and wearing your waders and wading boots. I use my Sage RPL, a 9ft 6 weight rod. You can also use a 5-weight rod, but anything less than that does not have what you need to land a big rainbow. The flies that I use are very small. They range from 20's to 24’s. It took me long time to learn to tie these small flies on my line. The way you rig your rod is you tie your point fly on the end of your leader, then tie a piece of 5X or 6X tippet on through the eye of your point fly and then tie on your dropper fly. Since the flies are so small I use a Turle Knot, which makes a smaller knot than my regular Improved Clinch Knot. You use a small piece of split shot and a strick indicator. Once you have accomplished this you are ready to fish. It is not uncommon to have a fish break you off and you have to rig again. The fish are so big and your tippet is small that you have to let the fish run. Once you hook a big rainbow, it can take you 15 minutes to land it. You have to let the fish run and when they stop then you reel in, you can do this many, many times before the fish gets tired enough to let you land him. It is very exciting and how I love to hear my line being reeled out when a big rainbow takes myfly and runs down stream with it. It makes my heart skip a beat. If you try to stop them they will always break you off and then you have to rig again. I have practiced enough and usually can do that in 10 minutes. That is a lot better than my 30 minutes it used to take me to re-rig. I try to get out of the water when I have to re-rig because the water is so chilly that my feet will get too cold when I stand in one place too long. Wading in the river is another venture. The river bottom is all river rocks with lots of green moss that grows everywhere. The moss is very slippery, so you have to watch where you are going. Needless to say I do not wade through the river very fast. The thought of going down in the river is scary so I am very careful. The water levels have been low which is nice for me. The river has been running at 350 to 700 CFS. When the river is low, it allows me to fish areas that I normally cannot do because of the fast current. The river flows below a mountain range. You park your vehicle off the road and then hike down to the river through the willows and standing water that has collected in different areas. In the cold months you have to break through the ice that can be two inches thick in the standing water areas to get to the river.
This river gets a lot of rods on it and it is not uncommon to see 40-50 fishermen in your eyesight. I have to say that I very seldom see another women on the river. I am not sure why. It is a great tail water fishery and if you like to catch big fish this is definitely a place to try. They also have float trip that you can hire a guide for. I have done a float trip in a boat, but I prefer to wade the river. I think I like this river so much because every time I go, it is different. The fish turn on and off so fast and trying to figure out what size fly, what color and how they want it keeps me very interested in the San Juan. You can also dry fly fish when hatches are going on. If you have landed 50% of the fish that you hooked for the day, then you have had a good day.
The flies I fish most often are: Flashback Pheasant Tail Nymph, San Juan Worm, RS-2's, WD 40, Zebra Midge, Olive Gold Ribbed Hares Ear, Midas Shrimp and Princess. I have to say that I been known to try anything when they are not biting. All you have to remember is that everything you fish is small and smaller.