Fishing Small Flies on the San Juan - Shawn McQuade

A popular and crowded river.


Western rivers are some of my favorite fisheries but they can also be challenging. Some of the most difficult fisheries are insect-rich tail-waters which form downstream from a dam.  Water releases from the bottom of the reservoir create spring creek-like conditions with consistent water temperatures and flows.  This is ideal habitat for year-round fishing, but tail-waters also produce selective trout habituated to both humans and specific food expectations. 

I was lucky to have worked at a fly shop on one of the most famous and difficult of these rivers, the San Juan in New Mexico. This river is home to so many trout that you can see the fish in the river while walking the banks. They are also not shy and I’ve had a fish peck at my waders while fishing in shallow waters. Keep in mind, these fish are not small. Naturally, there are some smaller-sized trout, but don’t be shocked when you see an 18- to 20-inch fish, cruising around like you’re not even there. 


Flies and Equipment

Because the San Juan gets a lot of angling pressure, trout are accustomed to seeing anglers. Similar to many tail-waters in the west, the fish here are selective, and fly size matters. Their diet is almost exclusive tiny midges. The water is too cold and close to the dam to hold the variety of insects found on most streams, including the ubiquitous caddis. Occasionally you do see a BWO hatch, but these are very tiny as well ranging from #22’s to #26’s. That’s small, but nothing compared to the midges in the San Juan. 


Size 30 compared to a size 16.


The main food source for trout on the San Juan River is midge larvae and pupae. These insect populations are ridiculously abundant, and trout will eat hundreds, possibly thousands, of these little snacks every day. Occasionally you will see a trout rise for a midge cluster, but most of the fishing is sub-surface using small nymphs. 

How small is small? Standard flies on the San Juan range from #24’s on the large size down to #30’s. Some anglers prefer to fish #32’s, if they can find the hooks. 

Fishing for 20-inch trout with a size #30 fly has its challenges. There is not much hook on such a small fly to grip the lip of the trout. And, as if to complicate matters, small tippets are required for the small hook eyes. Some hook brands offer enlarged eyes, but a size 6x tippet would be the maximum size for even the enlarged eye hooks. If you aren’t careful, you could easily straighten a hook, rip it out of the fish’s mouth, or snap your tippet with the slightest irregular pressure. Finesse is the name of the game.  

After a series of trials and errors, my favorite rod for the San Juan is an 11-foot Euro-nymphing rod, in a 3- to 4-weight. The longer, more sensitive tip helps keep tension on the line and provides more play when the fish runs. It also allows the angler to keep a soft, but constant pressure on the fish. 

When I first started fishing the San Juan, I was using a stiff action 9’ 5wt. I would land about 30% of my fish, and very few larger ones. But as soon as I switched to a longer, lighter action rod, my landing ratio increased to 70%.

The rod isn’t the only part of your gear to fine-tune. A reel must have a smooth drag. Yes, you could hand line in the fish, and many do. But I find far fewer fish are lost, and user error eliminated, playing off the reel with a very light drag setting.    


Fly Boxes

Success on the San Juan requires unusual attention to detail. The right fly boxes, for example, are critical.  Most fly boxes are not set up to accommodate such small flies.  Normal nymph fly boxes with foam or silicon slits are difficult to use because they engulf the entire fly making it difficult to keep or remove. Boxes with individual compartments work best like the traditional style dry fly boxes. They will also protect your flies if for some reason you drop your box.  Size #30 flies are difficult to find in the grass.  

The most useful boxes for carrying such small flies use magnetic-backed individual compartment boxes. This allows you to just throw the flies in the compartments and organize them in size and style. The magnets keep the flies from blowing away in a strong wind and keeps them from falling out if you accidentally drop your box in the water. The last thing you want is to drop a box filled with 100’s of small midges into the rushing water. 


Magnetic backed San Juan fly box.


Small flies, light tippet, large fish, and wind – all these variables add up, so nothing can be taken for granted. San Juan fishing has a way of exploiting these important micro-issues and can turn your day into a disaster.  It’s all about the details and approaching the river prepared.  As a commercial tier, I get the opportunity to tie and sell a lot of flies discussed in this article. I started to hear stories from my clients about the difficulties of keeping small flies safe on the water.  Out of necessity, I started selling magnetic boxes which have solved this problem for most clients. My customers rave about these little boxes, saying they no longer lose flies.  I’ve dropped my fair share of boxes in rushing water and have never lost any flies with the magnetic-backed boxes. A nice feature of these magnetic boxes is the sides of the compartments.  Because they are rounded, you don’t need tweezers or fumble around with fat fingers to remove a single fly. Just put your finger over the fly you want and pull it up and over the side of the compartment. This allows for easy selection of a fly and places it perfectly in-between your thumb and forefinger while you attached it to your fine tippet.


Subscribe or update to FTJ and receive this magnetic fly box. Measures 6 x 4 inched double sided!


Tying Wee flies

If you tie flies, you might be wondering, ‘How do I tie flies on such small hooks?’ Good question, but don’t worry, most of the patterns are very simple and only require a different level of sparseness than you might be used to.

Patterns like black beauties, zebra midges, and RS2’s are some of my go-to patterns. Red annelid patterns work very well and some are as simple as one material: a red thread covering the hook shank. With time and practice, you can tie most of these patterns easily. If seeing the fly in the vise is a problem I would suggest investing in a good magnifier. 

Walking to the river prepared means having a box filled with multiple sizes of any one pattern and being ready to make changes when nothing is working. Such days are common on the San Juan.  I could fish all day with a size #24 midge and never get a refusal. Then there are tougher days when I can’t get a look at anything smaller than #28 or #30. Make sure that whatever patterns you are tying, or buying, that you keep a few of each size. I often use a step-down approach to fly selection when the fish seem more selective than usual; start big and go small, as needed.


Fishing Techniques

I almost always fish under an indicator. Here you have lots of choices, but keep in mind these fish bite with an imperceptible feel.  Thingamabobbers work, but they lack sensitivity for the lightest strikes, which is often.  Most of the larger fish on the San Juan barely sip the flies and then spit them just as quickly. One of my favorite indicators is the New Zealand strike indicator system, which is a tuft of wool applied to the leader with a special tool. You can adjust the size of the wool for various levels of floatation, making it very sensitive. Under the indicator, I would tie a size #24-#26 red annelid, something like the Tav’s Big Mac, or the Skinny Annelid. When anglers think of fishing a red annelid on the San Juan River, they most often think ‘San Juan Worm.’  In my experience, the worm rarely catches fish; it’s just too large.  My secondary fly is a size #26-#30 black beauty or RS2. If I want the fly to sink faster, I’d put on a zebra midge with a tungsten bead. About 75 percent of my San Juan fishing uses this setup.  It works so well I rarely have to change flies unless I break off.   


McFly Angler fishing the San Juan.


Is it possible to hook into a few fish on larger flies? You bet, and there is no reason to not try it.   I’ve seen people come into the shop and purchase size #16 or #18 Zebra Midges and have great results on smaller fish, most under 14”.  Of course, that is a respectable trout throughout most of the American waters, but if you want to hook into some larger San Juan Trout, you really should step down in size. 

The larger, more experienced trout in that river has seen thousands of flies drifted past them. They probably have been hooked as many times and they learn quickly to avoid larger than normal midges, so stick to the size of the naturals.   


Brown Trout.


One is not always limited to midge fishing. I also throw small streamers like wooly buggers and rabbit zonkers with great success. This is especially true right after they stock the river with fingerling. The San Juan is stocked a few times a year, and if you catch the timing right, throwing a light-colored streamer into deep pools could end up netting you a very large brown trout. These browns come out of their deep holes looking for bigger meals during the week of these stockings. However, they don’t stock the river every week, and streamers aren’t always effective. 

When planning your next fishing trip, give the San Juan a try. I promise, you will not be disappointed, but you will be challenged.

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