Where to Fly Fish on the San Juan River, New Mexico (Maps, Flies and Technique)

The San Juan River is a fly fisherman’s dream, offering a bounty of opportunities to hook into rainbow trout, brown trout, and other species. This river is a unique blend of rapids and pools, each offering its own unique challenges to the angler. As a lifelong fly fisherman, I can tell you that the San Juan River is a true gem, and in this article, I’ll take you on a tour of the best spots to wet a line.

1. Texas Hole – Infamous

I didn’t see folks fighting, but any time you have trout “stacked up” like they are in the Texas Hole you’ll have some tension. The absolute best spot is just of the small island closest to the parking lot. Often a guide will send someone out early to “claim it” until a client comes down to the river.

During many of my trips I wasn’t able to jump into this honey hole so I made the wade across the river and fished on the north side of the river. Felt boots and a wading staff are a must. Hike up river a little ways to cross, the current is strong, but it’s not so deep you can’t make it.

The key to catching anything in this area is to get your fly down quickly. This means weighted flies or split shot and long leaders. The fish are deep holding near the bottom, which might be 7 to 8 feet down. The strong current is going to fight you getting those nymphs deep.

If you’ve never fished tiny nymph patterns the San Juan is going to teach you some lessons. Tiny 18 to 24 midge patterns are the ticket.

Guide Pro Tip: Here’s a little secret spot, walk down the boat ramp take 10 steps up river and drop a midge pattern in the run about 20 feet out. I’m not saying anything more – except hang on.

Guide Recommendation: James Garrett and the guys at About Trout (👈 link) “THE GUIDES” if you can’t get in James boat ask for Kyle. These guys have 200 plus days a year on the San Juan and guess where you’ll find them on many of their days off? You got it – fishing the “Juan”

2. Three Island Run – Tough to Wade, Perfect to Float

If you were to define the perfect run the Three Island Runs is it. One seam after another, the key is to drift deep and recognize the structure before your on top of it.

This section is tough to get to if your hiking in. It can be done, but you’ll be crossing some sketchy areas only to find out it’s nearly impossible to get a decent drift, in the best water from wadable areas.

Indicators with long leaders, heavy point flies like a tungsten beadhead mop fly and a trailing size 22 beadhead zebra midge. With the setup I just described you need to be able to adjust the depth fast. Adding a foot to the depth can mean success. I’ve fallen in love with Air-Lock Indicators (👈 link to Amazon) they’re easy to adjust, easy to remove, high floating and signal strikes well.

GUIDE PRO TIP: I have a Google Map with this spots tagged. Simple and easy, save it on your phone and start catching fish! Click Here 👉 Google Map for Fly Fishing the San Juan River

3. Lower Flats

In the Lower Flats the river slows and widens out.  I was on this stretch once just after a light rain.  Then something amazing happened – Flying Ants!  Like a switch, the trout turned onto dry fly ant patterns.

I caught a bunch of brown trout and lost a trophy in the mid-20-inch area easy.  It’s easy to talk about how big the trout are when you don’t have a picture to prove it.  😎

My best advice for this section when nymphing is to get your depth right and let your fly drift as naturally as possible without recasting.

There’s still great fishing all the way to the end of the quality waters section at Gravel Pit Day Use Area.

4. Upper Flats

If you’re looking for some adventure, upriver from Texas hole is an area called the Upper Flats.  Some of the biggest trout are taken out of this area, but with big reward, you’ll need to be okay with some adventure.

Look for the BOR parking and access signs along 511, you’ll scramble down an embankment on a switchback then hike a half mile through a wetlands area to the river.

The river is braided in this area and finding a good place to stand while still being able to reach the best water with a cast is difficult.   But you’ll avoid the crowds and some true trophies haunt these waters. 

If a size 20 is the smallest nymph in your fly box, don’t even go here.  A typical fly in this area is 22 to 26, this is technical water with difficult-to-reach seams.    

YOUTUBE

Why the San Juan is Perfect for Fly Fishing

Excellent Public Access

With nine public access points and campgrounds in the tailwater area, you won’t struggle with finding a spot to cast a fly.  The entire area is BLM land and is open for public use.  Perfect for a day of hiking and fishing.

Link to New Mexico Fishing Map 👉 https://nmdgf.maps.arcgis.com/apps/webappviewer/index.html?id=4af365eb03524e229de3eaf815fd56ca

Wade Fishing

Don’t let all the drift boats let you think you’ve got to float this river.  Yes, you’ll get the best shot at catching 50-plus fish in a from a drift boat, but lots of areas are available to the wade angler.  The Texas Hole is a perfect example.

Float – Like Bumper Boats

I’ve never seen so many drift boats launched as quickly as on the San Juan.  In the span of an hour, I saw over 40 boats dropped in…..

Deep nymph fishing is best from a boat.  Getting the fly far enough out in front of the boat to drift through the best runs for the LONGEST drift is the most effective method on this river.

Drifting down the “Juan” is the perfect day trip in a drift boat.  The distance isn’t so far as to make the trip uncomfortable.  The facilities for taking out are great and you can even stop at a couple of spots to use a restroom.   

What Kind of Fish are in the San Juan

The river is managed as a brown trout and rainbow trout fishery.  Thousands of pounds of catchable (10 inches plus) are stocked in the river annually.  The consistent cold water and steady stream flow are perfect for the bugs and trout. 

Favorite Flies for the San Juan

I’ve said it a bunch of times in this article. You’ve got to fish tiny flies, I know this might be new to you and it might be difficult, but these trout are eating tiny bugs. If you can master the tiny midge game in these waters you’re going to be rewarded.

Use big heavy nymphs as a point fly to get the offering down into the strike zone. Yes, you might pick up a trout or two with a big mop or big beadhead caddis.

Hatch Chart for the San Juan

Fly	Size	Start	End
Midge	18-24	All Year	All Year
Baetis (BWO) Nymph	22	March 1	September 1
Blood Worm	14-18	May 1	August 1
BWO	20	March 1	September 1
Caddis	18	June 1	August 1
Ants	16 – 20	June 1	September 1
Hoppers	8	July 1	September 1
Perdigon	20	July 1	August 1

• A note about ants, after a rain the hatch starts.  This can be some of the best dry fly fishing on this river.

The hatch chart is a general guideline and can vary based on water flow, temperature, and other factors. It’s always best to observe the river and the insects present to determine the best fly pattern to use.

Best Stream Flow for the San Juan

The best fishing conditions can be found right in the range that of 300 and 400 cfm.  Luckily this is right in the range that the flow is managed to.  Sometimes you’ll seasonal spikes, especially in mid-summer.  Trust that the weather isn’t going to kill a trip because of flow conditions.

Recommended Fly Fishing Setup

Nymphing Setup

Longer rods are nice, I used a 10-foot, 4-weight nymphing rod.  My TFO Drift worked pretty well here.  That extra distance allowed me to pick up the long leader and drop it into likely holding water.

You’ve got to think about your nymph getting down to the trout and if possible tapping them on the nose.  Heavy nymphs to drag down your midge and baetis patterns are a must. 

I used a 9 foot 5x tapers fluorocarbon leader with 4 feet of 6X fluorocarbon tippet.  This provided nearly 13 feet of leader to adjust the depth.  From my point fly (usually a heavily weighted nymph) I tied 12 inches of tippet off the bend onto a tiny beadhead nymph.

Dry Fly Setup

I love casting medium-fast dry fly rods, so you’ll see me using my 9-foot, fiberglass 5-weight.  I purchased a fly rod kit from Epic Fly Rods and built mine.  Most 9-foot, 5 to 6-weight rods will work perfectly.  If you have a 7-weight, that’s going to be fine.

With a weight forward floating fly line, I tied on a 6X, 9-foot nylon tapered leader.  From that, I attached my dry fly.  Again, think small, size-22 BWO and size-24 Griffiths gnats.   I start adding 6X or 7X tippet after changing out 3 or 4 flies.

New Mexico State Stocking Reports

New Mexico Game and Fish publishes a weekly fish stocking report.  The San Juan is on the report most weeks.  Thousands of trout per year are stocked in San Juan.  Stay in the “know” by checking out the stocking and the fishing report with this link – https://www.wildlife.state.nm.us/fishing/weekly-report/

Guides and Fly Shops

About Trout – I Highly Recommend getting ahold of James at About Trout (👈 Link).  If he doesn’t get you in his boat, he’s got a long list of excellent guides to set you up.  Like most great guides James books up a year in advance, so don’t delay.  Check out About Trout on YouTube

Fishheads of the San Juan – another guide service that’s been guiding on the San Juan for many years.

Rainbow Lodge – provides the guides, meals and rooms for a perfect San Juan River getaway.  The steak dinner is amazing!!  Full service and first class.

Last Cast

The San Juan River is a true gem for fly fishing enthusiasts, offering a variety of environments and species to catch. From the accessible Quality Waters to the remote and challenging Upper Flats, this river has something for everyone. With its clear water, diverse environments, and abundant fish populations, the San Juan River is a must-visit destination for the passionate fly fisherman.