Fall Fishing on the San Juan River is as Good as It Gets & Here’s How!

Fishing on the San Juan River in northwestern New Mexico can be at its best during the autumn months.

We were breaking ice that fall morning as we trudged through the marsh trail leading to the upper flats of the San Juan River.And we were hoping we’d get one of the more favored fishing spots to ourselves because the fall is when this trophy, trout stream really grows busy.

It’s when long, warm, sunny, days draw droves of eager anglers to the river’s fabled, quality waters below Navajo Dam in northwestern New Mexico.

But with a little strategy, some patience and a bit of luck, a determined angler can still enjoy the best the river has to offer along with some solitude to savor it.

Fall on the San Juan River in northwestern New Mexico.

The first thing we did to improve our luck was to schedule our trip for mid-November when the weather might be a little more unstable but the competition’s a hell of a lot thinner.

September and October are typically some of the busiest months on the river but right after Halloween and with the passing of day light savings time, things slow considerably.

Our weather cooperated with several warm, sunny, days accompanied by clear, cold, nights while the river produced great midge hatches on the top end and fabulous Baetis outbreaks further downstream.

We had set out that Sunday morning to fish a stretch of the river between Cottonwood Campground and Simon Canyon where numerous habitat improvements had been installed in recent years and the dry fly fishing has been reported great since the work was done.

Habitat Improvements on the San Juan River have vastly improved dry fly action in those areas.

We hoped to get in on some of the action and parked next to an oil and gas rig just down the hill from the old Dam Deli, Fly Shop and RV Park.

As we were putting on our gear a big Ford pickup sporting Colorado volunteer firefighter plates rolled up and parked right next to us. A couple of guys climbed down with their gear all ready to go and hurried off towards the river.

I called after them and asked if they thought there would be enough room on this side of the river for all of us and the big, beefy, driver just laughed back and said sure.

I was a little steamed at their jumping ahead of us like that so when we got down to the river and I found the truck’s passenger still standing there on the bank,  I walked up to him and asked him again if he thought there’d be enough room on this side of the river for all of us?

That guy seemed to get it and assured me that they’d make sure that we all had plenty of room and added that they could cross the river too.

A stroll through the cottonwoods below Simon Canyon on the San Juan River at Navajo Dam is a feast for the eyes.

So we left behind several goods runs and hiked upstream a ways before we started fishing.

This was one of the few drawbacks of the San Juan in the fall, it can get crowded and competitive, especially on the weekends.

While we were fishing this side of the river we spotted a crew of four anglers on the far bank, hiking downstream.

I looked back and saw the driver of the Ford pickup had crossed the river and was just wading into the water to fish the tail end of a series of rock structures over there.

His view of the anglers coming downstream was blocked by a wide, sweeping, bend in the river and thick stands of tall, dead, grass.

The group rounded the corner and pulled up upon seeing him and then then spread out in the water above him, taking the choice spots and leaving him nowhere to go upstream.

I smugly returned to my fishing and felt a tug on the line, the reel began to sing and a trout ran off with my rig.

The author shows off a typical San Juan River Rainbow trout.

When I looked up again after netting my trout I could see the angler who had worked so hard to get ahead of us was walking off downstream. Just an hour later the crew that ran him off wandered away too, leaving us a huge expanse of water to play in.

And we were rewarded for sticking it out that afternoon with a long running, Baetis hatch during which numerous trout residing around the rock habitat improvement structures rose to the surface with regularity.

We found that the currents flowing over, around and between the boulders formed by these habitat improvement structures could be challenging to negotiate with a dry fly but the results are spectacular for those who do.

Many trout rose to the fly including numerous browns of various lenghths and some big rainbows too.

We spent the remainder of the afternoon glued to this stretch of water, moving and expanding our reach as we picked off one rising trout after another.

We discovered when the sun was on the water that a #22, Parachute Adams worked fine and could easily be seen.

But when it became cloudy and the water took on a glare, a Blue Wing Olive fly  sporting a dark, CDC , post was the answer, its dark silhouette standing out on the glassy surface.

And as the hatch waned, so did the sunlight, so we headed back to the truck.

It had been a productive day and other than a steady stream of drift boat guides passing through, we saw few other anglers in the area except for the initial mob that morning.

We dined that night at Navajo Dam’s newest café, a restaurant inside the Fisheads fly shop where the “Build Your Own Burger” is a good meal and not a bad deal.

We ended the evening by sitting around a crackling bonfire, having a beer and talking about old times while listening to KNX AM out of Los Angeles.

Warm days and cold nights make for great fishing and camping on the San Juan River in northwestern New Mexico.

That night we slept soundly in doubled up sleeping bags nested atop thick air mattresses while our tents kept the frost at bay.

The next morning over instant coffee spiked with whiskey, we talked about the skimpy results we’d had during an earlier foray into the upper end of the river.

We decided to go back and give it another try.

But this time we would track down the state Game and Fish biologist stationed on the river, Marc Wethington, and ask him what the secret was to fishing the prolific midge hatches in the waters around the Upper Flats above Texas Hole.

Wethington, who does some guiding on the legendary river from time to time, shared with us his technique for capitalizing on the feeding frenzy that takes place during these upper river, midge hatches.

Marc Wethington is a Fisheries Biologist with the New Mexico Department of Game and Fish and has been stationed on the San Juan River his entire career.

Wethington advised us against chasing those fish feeding off the surface because of the time consuming, technical difficulty involved and the limited success rate.

These fish are tempting targets, he noted, and some anglers love the challenge and special reward that comes from catching such heavily fished and easily spooked trout.

But at any given time, the vast majority of trout are feeding below the surface, he stressed.

We needed to concentrate on them if we wanted to be more productive in this stretch of water.

Wethington told us his typical set up for midge fishing during the fall is a basic black and red combo.

Any typical, black, midge pattern in size 22 through 28 tied below a similarly sized, red larva, Disco midge or Red Hot would work, he said.

Wethington said he prefers his black midges tied on a scud hook with a sparse, silver, wire wrap and a crystal flash wing tied in behind a black, dubbed head.

A red version of this same fly, referred to by some as a Disco midge, can also be used but with red thread substituted on the body and peacock herl used for the head. The silver wire wrap and crystal flash wings are used on this fly too.

And factory produced, red hooks wrapped in very thin, green, translucent micro tubing make for good red larvae while a red wrapped scud hook with a red bead head makes for a good Red Hot, he said.

Minuscule weights and micro-flies make for successful fishing on the San Juan River below Navajo Dam in northwestern New Mexico.

Check the local shops for variations of these types of flies or whip up some samples of your own based on fly patterns found online.

And if the water is off-color, try substituting a small egg pattern in any number of colors for the top fly and use the other flies as droppers, Wethington said.

But the real key to fishing the upper water during these midge hatches is to keep the flies suspended off the bottom, up towards the middle of water column, where the trout are more likely to be feeding.

Many anglers make the mistake of using too much lead and dragging their flies along the bottom in these heavily fished upper waters, he says.

The use of a number 8, micro, split shot (0.06G) is essential for use in Wethington’s rig with the split shot riding about 10-inches above the top fly and the dropper fly tied about 10 to 12-inches below.

Tippet should be 6x or smaller.

The strike indicator is also important and it should be small like a Palsa pinch-on or a small, Hot-Head indicator which is placed another foot or two above the split shot and then adjusted for the depth of the water being fished, typically at about one and a half times the depth.

The bottom line is to use microscopic flies on light tackle and allow them to dead drift at varying heights through the water column, he said.

Wethington tied up one of his rigs for our rod and then offered one  last bit of parting advice, strike early and often and at any sign of hesitation, stoppage or dipping by the indicator.

And use a gentle hook set by just lifting the rod tip straight up so as to not pop out the very small, barbless, hooks, he added.

View overlooking Baetis Bend on the San Juan River during the fall months.

So as we broke through the ice that morning, my partner’s rod was all set to go with Wethington’s rig and we were confident about trying it out.

We hiked through the marsh until we pushed our way through the willows and emerged just above the upper flats where we found a shallow, slow moving side channel to our right, a couple of islands dead ahead of us and the main stem of the river to the far left.

We were all alone and immediately set out for the islands where we had seen anglers enjoying some success a few days earlier.

My partner took up position where a channel cuts between the two islands and rolled his rig into the water where we could see trout feeding below.

The strike was immediate, as was his disappointment, as he broke off the whole rig with a mighty jerk of the rod.

My buddy, a bass fisherman, was livid, even more so when I told him we didn’t have any more of those flies or the little weights because I’d mistakenly left them all back on the hood of the truck.

I was only kidding but he didn’t know that as I made a big show of searching my vest pockets and mumbling about my stupidity.

I soon ended the charade and we had a great morning fighting trout in the upper flats of the San Juan River with our new found knowledge of how to fish there.

TA Phillips shows off a fat San Juan Trout he bagged using the Wethington method.

And it was a beautiful, fall day.  Warm and sunny with a piercing blue sky and very, few if any other anglers to distract us from our fishing on that weekday morning.

Tips and Tricks for Fall Fishing on the San Juan River:

Try to schedule your trip during the week but either way, the real battle will be the weather and your clothing.

You have to be able to accommodate extreme temperature swings and rapidly changing conditions. One minute it may be wet and windy and the next, sunny and warm.

Layers are essential, as is a fishing vest that can handle carrying some extra clothing.

At the very least a windbreaker or light raincoat over a fleece or wool sweater atop a thick sweatshirt should suffice. I like to wear a fleece vest too. Strip or add layers as required.

Bring along fingerless gloves to keep your hands warm and a warm beanie to pull over your baseball cap if it gets cold. Keep your feet and head warm as it is the best way to battle the cold.

Stash an extra change of the clothing back in your vehicle just in case you fall in, if you don’t, you probably will.

Wear polarized sunglasses so you can see through the water to the riverbed below and to also protect your eyes from the sun.

The San Juan River flowing south below the village of Navajo Dam.

Thick, neoprene, waders are good if you intend to stand in one place for long as the San Juan is a consistently cold, tail water. The use of breathable waders will require a thick set of fleece pants or wool long johns underneath.

Those who like to hike and fish might be better off wearing a pair of hip waders over jeans with wool/synthetic long johns underneath.  The San Juan River is easily navigated in hip waders during the fall due to consistent, lower flows.

Remember to wear good, thick, socks made of wool, fleece or neoprene and leave your boots loose enough to allow blood and air to circulate.

Force yourself to drink plenty of water as the climate here will dehydrate you quickly. Limit alcohol and caffeine intake, both contribute to dehydration.

Energy bars, trail mix, beef jerky, cheese, peanuts, apples, etc. are all good foods to carry and keep you moving and warm.

Back at camp keep in mind the sun goes down early and it might be easier to whip up a can of stew or some chili rather than to fire up a grill and burn some steaks because they’ll grow cold fast and won’t be as soothing

There’s plenty of camping to be found on public lands adjoining the san Juan River.

Don’t pass up any loose firewood you come across, grab it because there’s nothing like a good campfire to warm those tired bones and lift the spirits as the sun drops behind the mesa and the day fades away.

Carry a headlamp for hands free lighting and don’t forget the extra batteries.

Bring your beanie cap to bed to keep your head and ears warm overnight. Wear your fingerless gloves too, so you’ll be comfortable while reading in bed. Don’t forget a good book, reading lamp, extra batteries and plenty of pillows.

Guys should keep an empty water bottle inside the tent; it’ll save them the hassle of getting up in the middle of the night to take a whiz. Just don’t mistake it in the morning for your other water bottle, the one you kept under your bags to keep from freezing so you can make coffee in the morning.

Bring along your wool/fleece booties or slippers, they make getting up in the morning a lot easier and are more comfortable to put on than a pair of cold, hard, hiking boots.  Keep those long johns on too for wandering around camp.

Fabled ET Rock on the San Juan River at Simon Canyon.

Pack hot cocoa, tea, instant coffee, non dairy creamer, sugar, a small cooking pot and a good sized coffee mug so you can have a hot drink in the morning to get you going.

I use a burner and stand that attaches to one of those, one pound, propane canisters. It lights up quick, burns hot and lasts a long time. My wife turned me onto this and I haven’t used my white gas stove much since.

Eat a good breakfast while you’re waiting for the river to warm up. You won’t regret it come noon when the fishing is kicking up and your stomach isn’t. Hard boiled eggs, cheese, apple slices and beef jerky make for an easy morning meal.

If it threatens to snow or rain during your trip, don’t cancel, as the San Juan River produces some of its best fishing during inclement weather.

If nasty weather threatens, try to get there before it hits, be there when it does, then leave after it passes. Rent a room if need be and enjoy the fishing and freedom a fall, storm can bring to the San Juan River.

A San Juan Country Road basks in the sunshine of a gorgeous autumn day on the San Juan River in northwestern New Mexico.

Originally published in Outdoors New Mexico in November 2011.