Fly fishing guide Mike Allen was sitting quietly on his kayak on the wide open waters of Mission Bay, fly rod in his right hand. With his left, he periodically twitched the line, causing the tiny pink fly unseen at the end to dance along the bottom. Suddenly Allen drew the rod back, and his face lit up as he whooped in delight. A spotted bay bass had snapped up his imitation ghost shrimp. Typical for the species, the small fish was putting up a spirited fight.

Allen’s fishing partner and fellow guide Dennis Farrier watched from nearby. As the battle continued, I remembered what Farrier had told me earlier about fly fishing. “You can’t fish a fly rod like a conventional,” he’d said. Fly fishing is a finesse game, a struggle on even ground. The tackle is matched to the quarry so fish can’t be powered in, but must be carefully played, making each catch a satisfying accomplishment.

Wearing a broad smile on his face, Allen scooped up the 12-inch long spotted bay bass. It was far from the largest fish he’d ever caught on the fly, yet it didn’t look as if Allen could be any happier. That could be because he’d just proved his point that Southern California’s bays offer fine sport for fly casters. It’s a backyard opportunity that some area fly fishers overlook in their zeal to hunt trout up in the Sierras or some other prime high country fly water. The better fight is right here at home.

“To me there is no comparison between saltwater fish and trout,” said Allen. “Saltwater fish are like trout on steroids. Their life is eat or be eaten; they’ve got to be pretty tough.”

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The local bays also provide a gentle introduction for those taking up the sport. A precision fly cast isn’t required. In most cases all you have to do is hit the water. Working the wet flies used for the local saltwater bass and halibut isn’t overly technical either.

“It’s actually easier than fly casting in the Sierras,” said Allen. “The fish are at home on the bottom. Once you get the fly down there, all you have to do is move it along the bottom by drifting or striping line.”

The flies of choice for fishing Southern California’s bays imitate baitfish or crustaceans. Since the saltwater fly scene is still something of a frontier, there is a lot of room for innovation. The pictured ghost shrimp imitator is a perfect example. Known as the DUI, it was originated by Doug Uyematsu of the Long Beach Casting Club.

Fly Fishing Kayak Style
Fly anglers can float Southern California’s bays on boats, or patrol the shoreline shallows in pursuit of fish. Allen prefers to use his Hobie Mirage Outback. Fly fishing the bays from a kayak is “Gorgeous, stealthful, quiet, beautiful. We love it,” said Allen.

“You can catch anything from a flyrod, and just about anything from a kayak,” chimed in Farrier.

Other than the aesthetic reasons, the obvious advantages of fly fishing the bays from a fishing kayak are the low cost and maintenance load relative to owning a boat and the ability to access skinny water. But the fly angler will most appreciate the stealth factor. No craft is quieter.

There are a few downsides that must be accommodated. It is more difficult to spot fish from the low vantage of a kayak cockpit. Casting from the seated position takes some getting used to. Kayak anglers who have mastered standing and casting have no trouble with either. For paddle-powered anglers, kayak control can be frustrating, because it is difficult to hold a precise position against current or wind. Allen solves that problem by using a pedal-powered Hobie MirageDrive kayak. Instead of putting down the fly rod and picking up the paddle when he drifts off a spot, Allen just kicks lazily to remain on station.

Managing the loose line stripped from the reel while working the fly can be an issue. The coils are prone to snag on seat hardware, rod holders, paddle keeper clips, and other deck clutter. Allen says most kayak fly anglers keep the deck forward of the cockpit as clean as possible to prevent problems. Rod holders, and you’ll need at least one specifically designed to hold a fly rod, should be installed out of the way behind the cockpit.

If you prefer to do your fishing while sitting down, casting a fly rod from the confined seat of a kayak can be tough for those still developing that illusive perfect form. According to Allen, turning the problem on its side vastly simplifies the issue. Instead of facing forward, sit side-saddle with your legs dangling in the water. Scoot forward a bit. Strip line into the empty seat. Hardware in the way? “Lay a beach towel over it to lessen the chances of snagging the line,” advises Allen.

Basic Tackle for Fly Fishing the Bays
Allen uses a 7-weight fly rod in the Southland’s sheltered saltwater. A 6 or 8-weight will get you by. Allen’s bay rod is the typical 9-foot model.

Most of the predominant bay gamefish lurk near the bottom. To target halibut or the saltwater basses, bay fly casters need a way to get their insubstantial flies down to the strike zone. There are two options. Some go with sinking line. Allen prefers to tie a sink tippet onto floating line. He feels this setup provides better action. Instead of draping along the bottom like sinking line, the sink tippet hangs down from the floating line. When Allen gives the line a twitch, the fly briefly hops and skips across the bottom.

Like virtually every other bit of gear pertaining to the rod or line in fly fishing, sinking line or tippet carries a numerical rating. In this case it indicates how quickly or slowly it sinks, expressed in IPS or Inches Per Second. Allen normally uses 4 to 5 IPS tippet. Consider the implications. After making a cast in 12 feet of water, Allen has to wait about 30 seconds for the fly to hit bottom before he can start his retrieve.

The fastest sinking tippet generally available is 7 IPS. The maximum practical depth to fish bottom or structure-hugging spotted bay or calico bass in the bays is 25 to 30 feet, dependent of course on favorable wind and current.

Between the fly and the sinking tippet or line you’ll need a leader. In the bays, where the fish strike hard, Allen doesn’t bother with the gossamer-thin 7X threads typically used to target wary trout. Those have a breaking strength of only 1 to 2 pounds. With a breaking strength of 4 to 5 pounds, 3X to 5X leaders are a better choice. Perhaps the best bet is to go with conventional leader material. Allen uses 6-pound test fluorocarbon in lengths of 5 to 6 feet.

Most flies fool fish by replicating the natural forage. In freshwater, bits of feather and tufts of fur and fluff are often tied into tiny lures that resemble minnows or aquatic insects. The minnow masqueraders carry over to the saltwater that fills Southern California’s bays. For an example, Allen points to the various clouser patterns in blue or chartreuse and white. In the salt, the analogues to the insect imitations are flies that look like shrimp or crabs. Here reds and oranges are common.

Cast your fly towards a likely area, and then count it down to the bottom. Once it is there, the action to impart depends on the type of fly used. Allen makes short 5 to 6-inch strips every few seconds when he’s baiting a shrimp imitation. Minnow imitations like clousers are pulled in faster with long strips of a foot or two. The erratic action mimics an injured baitfish.

For a beginner, fly selection can be bewildering. Not to worry, your local fly shop will be happy to provide you with a basic selection. The horizon is wide open for experienced freshwater fly-tiers. Allen says saltwater fly design in Southern California is still something of a frontier. There’s quite a bit of innovation and experimentation taking place.

Bays to Try Casting a Fly
From San Diego in the south all the way up to Ventura, Southern California’s shoreline is dotted with sheltered saltwater suitable for kayak fly fishing. For the bottom stitching methods described here, anglers will have the most to target in San Diego Bay, Mission Bay, the Dana Point Harbor area, and Newport Bay. There’s solid flat water fly angling farther north in King Harbor and other places. Here, fly anglers will probably prefer to target fish that swim higher in the water column such as barracuda and bonito. Check in with your local fly shop for more information on the appropriate flies and methods for those species.

San Diego
The “Big Bay” is a tremendous sport fishery. Much of it is far too deep for fly fishing the bottom huggers, but there are plenty of shallows along the main channel margins. Launch from Shelter Island or Spanish Landing in the north bay to fish for spotted bay bass amidst the marinas and side channels. Or cross the bridge onto glitzy Coronado Island, where you can put in at Tidelands Park or on the southern side of Glorietta Bay across from the Hotel Del. Here again spotties are the main targets, but a variety of other gamefish might take your flies. This area is one of Allen’s favorites. “A lot of the time you’ll catch 30 to 40 fish a day,” said Allen.

The warm and shallow southern reaches of San Diego Bay, accessed via Pepper Park, the Chula Vista Marina, or Chula Vista’s Bayside Park, give up fast action on smaller spotted bay bass. They can come cast after cast in what Allen calls “total fish contact. That’s fish after fish, I just love it.”

There are halibut too, the biggest in the bay, and sometimes marauding schools of yellowfin croaker breeze through. But there’s no question the feature attraction is the possibility of tangling with bonefish. It’s not the same as sight-fishing to big bones on some Caribbean isle’s flats, but these smaller fish will still give you a tackle-testing battle. Try ghost shrimp imitators

San Diego’s Mission Bay offers the same finny quarries as its bigger neighbor, but in a more sheltered, forgiving setting. Most of the bay is no more than 15 to 20 feet deep. Find the thick eel grass beds and you’ve likely found the fish.

Orange County
Orange County offers two prime spots, Dana Point Harbor and Newport Harbor. Dana is the smaller of the two. Miles of shallow flats dotted with reefs holding calico bass wait just outside the harbor mouth. Launch at Mother’s Beach or just outside the bay at Doheny State Beach, but don’t overlook the marina. “I’ve taken clients who’ve caught legal white seabass in the harbor. Dana is a good fishery,” said Allen.

Newport is a lot like Mission, another bay that was created largely through dredging. The outer waters are surrounded by multi-million dollar homes with private docks for motor yachts. The spotted bay bass take no note of the glamour; they make their homes amid all the artificial structure. According to Allen, this is another excellent fly fishery. East of PCH, the watercourses are much more estuarine and the structures natural. Get your kayak wet at West Bay Avenue, Coast Guard Beach, or the Newport Dunes Resort.