While I've mentioned fishing the San Juan river in northwestern New Mexico a couple of times before, I haven't been over there much in recent years. When I first started fishing the river and figuring that fishing out, it was one of my primary destinations and I'd spend ten or more weekends up there every winter. I quickly learned that I preferred to fish winter and early spring when cold temperatures and higher flows, respectively, keep the crowds down. In recent years the spring flows have been low and some of the winter flows really low, down to 250 cfs, rather than a more-normal 500 cfs, so I've stayed off the river. However, the last couple of years have benefited from more normal flows, so the fishery should be in a little better shape.
I can't say that the fishing has exactly palled, but it has changed a bit for me. Ten years ago, if you'd have told me that I'd go over a year without spending a weekend on the San Juan I'd have thought you were kidding. Guys that I talked to in the fly shop that "just don't get up there any more" struck me as oddly spoiled- not go spend a weekend catching two pound trout? Now I'm one of those guys. The river is still worth a trip.
The fishery on the San Juan below Navajo Dam is pretty famous. The water flows at a constant 42 degrees F, thanks to the bottom-draw dam and deep reservoir behind it.
The constant water temperature results in year round growth of aquatic insects and the trout that feed on them. Because the water is quite cold, there isn't a great variety of insects (at least from a fly fishers perspective), mostly midges and annelids. However, cloudy days in the colder months will frequently see a blue winged olive hatch, particularly about halfway down the catch and release section, so you can get some dry fly fishing every now and again.
While there is only limited natural reproduction in the river, the New Mexico Dept. of Game and Fish stocks fry and the population is quite dense, with the average trout caught running about fifteen inches and over a pound. The upper portion of the river is also primarily a catch and release fishery, with the limit being one fish over twenty inches and the culture strongly against keeping that.
Because of the large numbers of big trout, the river sees incredible pressure. Fishermen from around the country and around the world travel to the San Juan. All those fishermen result in a crowded situation and you have to adjust your concept of personal space a bit and not get offended if someone comes fairly close to you, much closer than you would be happy about if on a more remote river. One way to get away from others is to fish the high spring flows. Once the river gets above 2000 cfs, the number of people fishing it goes down substantially. At 5000 cfs, you can have decent stretches all to yourself and the fish have a lot of current to beat you with. Of course, you also have to wade very carefully and generally stick to edges and backwaters. The wading up there is complicated by a very healthy growth of bug-feeding moss, which renders the cobbles and especially the occasional sandstone stretches quite slippery. Don't walk on the black-colored moss- if you do you'll almost certainly fall and that cold water just about requires a trip back to the truck for dry clothes.
I think that a five-weight is about the lightest rod you should use up there. Some of the really fast, high end rods rated as four-weights would also be fine, but a five or a six is generally better. Because it is a catch and release fishery that sees tremendous pressure, it is imperative to get the fish in quickly, in the best shape possible, and release it with as little harm as you can. If you get a fairly hot fish, there's no way you are going to muscle it on a three or four weight. Of course, the other limitation is you tippet. I try to fish top quality 5x, which lets you put quite a bit of pressure on your gear. With flies smaller than size 20, I have to go to 6x. I'd rather break a few fish off getting them in quickly than leave a wake of doomed trout behind me, so I lose quite a few more flies with 6x. I know of guys who use 7x or finer, but I won't do that up there.
The basic rig is a nine-foot leader, to which you tie a dropper and point. For a 5x leader, I use a surgeon's knot to tie a sixteen inch length of 5x material to the end of the leader. You want the tag end of that added length to be about four inches long, but no more than that. You tie a San Juan Worm up there, and the short length keeps it from tangling too badly. Down on the point end, you tie a small nymph imitation, something size 18 or smaller. A couple of inches above the knot, crimp on a split shot, then, about a foot down the leader from your fly line, attach the strike indicator of your choice. You'll end up changing the shot quite a bit, adding or taking it off, as you want the flies to dead drift in the current just above the bottom. They should hang up every third or fourth drift. If you never hang up, you aren't fishing deep enough and you're missing a lot of fish.
You can do pretty well on the river with a pretty basic fly box. The one fly that I've most consistently caught fish on up there is the Chenille San Juan Worm in a dull orange color. Tied on a #14 nymph hook with no weight, you cover the hook shank with red thread (6/0), then cut a piece of ultra chenille about 1 1/4 inches long, which is tied in at the back of the shank (keep the tie in narrow), the thread spiraled up to a bit behind the eye of the hook, then tied in again. You whip finish under the chenille, then use a match or lighter to melt the ends of the chenille to points. You need a lot of these flies, as the chenille becomes floppy with use and once it starts folding back on itself the fish don't like it much.
For days when they just don't want a chenille worm, you can try TJ's Sparkle Worm, in orange or red.
For smaller stuff, it's pretty hard to beat a foam wing emerger. You want to tie them in chocolate brown, black, and grey and in sizes 18 and 20, perhaps 22. Personally, I think a tail of two or three evenly spaced muskrat guard hairs is important to this pattern, as it helps the fly maintain a natural orientation in the water.
Small thread-body nymphs are also good, try wrapping the thread body with a single layer of clear flashabou on a few and use a single turn of peacock herl or a tiny bit of dubbing for the head. Tie them in 20 and 22.
Last, you also want a few size 8 to 12 black woolly buggers or rabbit hair leaches. Some days they don't want the worms, or the water is a bit off color, and the buggers or leaches do really well.
Still scenic, especially during the months with fewer people:
The latest edition (available in pdf) of the New Mexico Wildlife Federation's journal reports recent problems with the San Juan, which they link to the vast increase in oil and gas drilling since the days I was spending a lot of time on the river.
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