Below Navajo Lake near Farmington, New Mexico is one of the most popular fly-fishing destinations in the state: the San Juan River. This superb tailwater fishery holds over 70,000 rainbow trout in the 3-mile stretch known as the "Quality Waters." The average fish is a healthy 17 inches. The San Juan's stable year-round water temperature (about 42 degrees) and abundant insect life account for the phenomenal growth rate of its trout. The fish feed year 'round, and the fishing can be fantastic in any season.

But in recent years, springtime high flows of 5,000 cfs (cubic feet per second) have made for some difficult, if not dangerous, wading conditions. The reason for the high flows is the Division of Wildlife's ongoing and controversial "squawfish study." The flows in the San Juan are raised from the Navajo Dam to match the Animas River simulating a "natural" spring runoff for the Colorado squawfish and razorback sucker-two threatened native species.

During winter, the river averages about 500 cfs and has been as low as 250 cfs in recent years. Fishing at those levels can be very easy-70,000 fish don't have a lot of places to hide. But at 5,000 cfs, that great fishing hole that was so good to you the last time you were here is now inaccessible or completely blown out by the high flows. The fish are still in there, but where are they?

I spent two days on the San Juan during the springtime high flows and found the fish and what they were feeding on-but not without the help of some local experts. The trick, they showed me, is to fish the newly-flooded shallows and backchannels.

During lower flows, the shallows above Texas Hole are mostly swamps and mud. But when the flows from the dam are raised, the water rushes in and churns up fish food. Trout then move in to get their fill. Black flies and river midges are the trout's main food sources, but San Juan worms, cranefly larvae and carp and trout fry are abundant as well.

I fished the first day with Farmington local Steve Gardenhire. We parked at Texas Hole and waded upstream through Kiddie Pool, where about fifteen people were bottled up at one end. None were catching fish. "When the water's this high,'' said Gardenhire, "you'll see people using other fishermen to find the fish. One guy hooks into a fish and the crowd moves in on him. We're moving upstream."

Above Kiddie Pool, the river fingers out between dozens of small islands, forming rivulets, seams and riffles. Steve suggested using a tandem of a San Juan worm and an annelid. Annelids are midges in the larvae stage. They're bright green most of the time, but towards the end of the larvae stage, their bodies fill with hemoglobin and they turn bright red. Below the San Juan worm I tied on a size 20 green machine (a flashy-green body with a black-dubbed head). Steve tied on a size 20 red hot (a red-bodied pattern with silver-wire ribbing and a small clear or red beadhead).

I worked along the seam of a long, shallow riffle. After a few casts, my strike indicator twitched. I set the hook and hauled in an 18-inch rainbow. He had hit the green machine. A bit later, I hooked into the biggest fish I would see all weekend. He raced past me downstream and thrashed in the shallows. Instead of walking towards him and netting him, I tried to play him back to me and he shook my fly off. Live and learn.

The good fishing lasted into the afternoon. Storm clouds were moving in when Gardenhire called me over to him. He pointed to a long riffle that flowed into a circling eddy. Midges were hatching and being blown across the surface by the increasing winds. We saw countless fish feeding subsurface on the emerging insects. Occasionally, one would rise to the top for an adult. I tied on a size 18 Para-Adams and size 20 RS2 dropper (a gray-bodied emerger pattern with a foam wingcase and split tail).

We took a number of good-sized fish in this area over the next hour. They were suspended about six inches below the surface and were easy to spot. Most took the nymph, but I did get three to take the dry. It started raining and in a matter of minutes I was completely soaked. But I hardly noticed, I was having such a good time. It wasn't until the lightning began that we headed back.

The next morning I set off with Tom Teushert, a guide for Rizuto's San Juan River Lodge, and Peggy Harrell, one of the first female guides in New Mexico. Launching the boat at Texas Hole, we floated downstream towards the serene and rarely fished Third Channel-an area inaccessible by boat except during the highest flows.

Teushert handed me a brown-bodied beadhead wooly bugger with a gold-tinsel and marabou tail. He said that he first used this pattern at some lakes in Colorado, and discovered that it worked even better on the San Juan as a minnow and cranefly-larvae imitation. Below the bugger, I tied on a size 18 red hot. We drifted past a group of people fishing the main channel and veered left into the quiet isolation of the Upper Estuary. The Estuary split into two channels, the Second and Third. We cut left again and entered the Third Channel.

Casting into the reeded areas along the shore, Harrell hauled in several fish before I even had a strike. I asked her what I was doing wrong. "Don't strip in line and swim your bugger," she said. "Just hop your indicator along in its drift to pick your flies up off the bottom. Flip it forward a few inches. They usually hit it right after the hop."

She was right. Popping the flies off the bottom generated some monster hits. They weren't the subtle strikes I was getting the day before. These fish were very aggressive and put up a stubborn fight. "These rainbows down here fight a lot harder,'' she said. "There not used to humans and not as tame as the fish in the main channel. They just don't give up on you."

Clouded water and rainy weather prevented us from getting any dry-fly action that day. But under better conditions, the backchannels attract egg-laying insects. They told me that because there isn't much oxygen in the slow-moving backchannels, most of the insects remain in the first two stages of life: larvae and pupae. But when the bugs hatch in the faster, oxygen-rich currents of the main channel, they migrate over to the backchannels to lay eggs. Terrestrials are also plentiful in these areas because of the thick vegetation along the shore. Some of Teushert's other favorite patterns for the backchannels are leeches, olive wooly buggers and damsel nymphs. Again, hopping the indicator is vital.

If you want to wade the backchannels, park in the day-use area off Highway 511 between Lower Flats and the church. It's a short, but muddy walk down to the Upper Estuary. Beavers dam up the Third Channel when the water begins to drop, so the fishing can still be good there. But the mud makes the wading a little tough.

The flow rates for the spring of 1998 should again be as high as 5,000 cfs-unless the snow pack in the San Juan Mountains and subsequent spring runoff in the Animas are unusually low. But don't let high flows keep you away. They offer the opportunity to discover new areas of the river and new fishing techniques which are otherwise unavailable.

Wes R. Smalling is an outdoor writer and fly-fishing guide from Santa Fe, New Mexico. His fishing report appears weekly in the Santa Fe New Mexican newspaper. This is his first contribution to Fly Fish America.
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