Fishing for San Diego Bonefish

The bonefish of San Diego Bay are plentiful and eager to fight.
San Diego bonefish

San Diego bonefish

Bonefish — synonymous with the shallows of Florida and the tropics — are also plentiful in the Pacific, if you know where to look and how to fish for them. San Diego Bay makes an excellent starting point for expanding your bonefish horizons.

Ah, a tap! A bonefish nailed the bait. I set the hook, and line hissed through the water as it melted from the light spinning reel. My hands trembled, and I felt my heart in my throat. Though the setting was unlikely, this was my first bonefish.

Mention bonefish and most anglers think of clear, radiant flats and tropical destinations like the Florida Keys, Bahamas, Christmas Island and San Diego. Wait. San Diego? For bonefish? Really?


Yes, really. We’re talking about ­California’s San Diego Bay and chrome speedsters that look nearly identical to bonefish of the tropics.

“Relatively few people realize that San Diego Bay has a healthy population of bonefish and that you can catch them year-around,” says Capt. James Nelson, who specializes in guiding anglers on San Diego Bay.

While they look like transplants from Florida, these bonefish aren’t the same variety you catch in the Keys, or even at Christmas Island in the Pacific. The species in San Diego Bay is known as the Cortez bonefish, more ­diminutive than its cousins but still a beautiful and challenging light-tackle quarry ­— one that has long held a spot on my bucket list.


A chance to cross it off came this year with Nelson, who targets bonefish aboard his 24-foot bay boat. Not only did I land my first bonefish, we went on to catch-and-release seven more of the hard-fighting bones in a single morning of fishing. Nelson says he has had days when guests have caught more than 20 bonefish, proving the vitality of the San Diego bonefish population.

But they are not always easy to catch. A number of ­elements help improve your chances of success, starting with the right bait.

** Baiting Up**


“I thought you’d want to see this,” says Nelson as he puts the bow of the boat on an exposed mud flat near the mouth of the Sweetwater River before we head out to fish. He pulls out a device that goes by names such as slurp gun, yabbie pump and mud sucker. It’s a tube with plunger inside. Stick it in the mud, and pull up on the plunger handle to suck up a cylinder of goo. Then push down on the handle to eject the mud, and paw through the muck to see if you caught one of the bonefish’s favorite foods: ghost shrimp. The technique works best on mud and sandy back-bay areas exposed at low tide.

Nelson hops out of the boat and goes to work, ­slurping up 50 ghost shrimp (the maximum daily limit per person in California) in about 15 minutes, putting the two-inch-long crustaceans in a small bucket of salt water to keep them alive.

According to Milton Love, Ph.D., with the Department of Marine Biology at the University of California, Santa Barbara, Cortez bonefish prey on a wide range of creatures, including amphipods, crabs, worms and even small gobies. However, ghost shrimp are relatively easy to obtain (you can also buy them at some bait shops), and so they have become the ­preferred bait among San Diego bonefish specialists.


With our bait on board, we motor out of the mouth of the Sweetwater River, and Nelson turns south and heads into the shallow lower reaches of San Diego Bay, an area encompassing approximately four square miles, separated from the Pacific by a spit known as the Silver Strand. To the east are the shores of Chula Vista, the last city before the Mexican border at Tijuana.

** Fish the Edges**

In this region of the bay, the bottom is pockmarked with craterlike depressions, according to Nelson. “There are big holes throughout the lower bay, 20 to 30 feet in diameter and 20 to 30 feet deep,” he says. “I often meter lots of fish in the holes on the fish finder, but these fish rarely bite. Instead, we usually catch bonefish up on the edges of the depressions.”

Water depths favored by bonefish in San Diego Bay vary with the time of year. Nelson finds that once you ­discover the right depth, the bites come fast. “I usually start in eight to 10 feet of water, but will move to six to seven feet if we’re not getting bit,” he explains. “If you’re not getting bites, try a different area, as the bonefish are always around, but you need to find them. Sometimes you need to go even ­shallower — say four or five feet.”

“Cortez bonefish like to poke around in eelgrass, as well as in sand and mud,” says Love. “So these are the types of habitats you should focus on if you want to catch bonefish in San Diego Bay.” The fish are generally looking down for food, so keeping the bait close to the bottom is important, Love says.

** Rig for Drifting**

Because these fish inhabit deeper, murky water rather than clear, shallow flats, traditional sight-fishing methods don’t work well in San Diego Bay. Instead, drift-fishing is the preferred technique. It’s an effective technique, as bonefish eagerly inhale the shrimp we drift past them, sometimes even jumping on just pieces of bait. “They don’t miss many chances to eat, even if it’s just a morsel,” says Nelson.

San Diego bonefish aren’t nearly as spooky as their East Coast cousins. “I tell people, don’t cast. Just drop the bait straight down and try to keep the line as vertical as possible,” he says. “Many times, they will get a bite right under the boat.”

** Currents and Clarity**

Surprisingly, water movement has little effect on the feeding habits of bonefish. “Current is unimportant,” says Nelson. “Unlike other bay species such as halibut, yellowfin croaker and spotted bay bass, bonefish seem to be out looking for food all of the time, whether or not there’s water moving.”

Love agrees: “My observations of the species in Bahia San Quintin on the Pacific coast of upper Baja California indicate that Cortez bonefish are not necessarily current driven. I also believe they don’t care about visibility, as we have caught them in turbid water.”

However, Nelson’s drift-fishing technique is aided by current and/or wind, as it helps keep the bait moving. The wind on San Diego Bay usually blows out of the west, and in the afternoon, it can get pretty strong. On these occasions, Nelson likes to deploy a drift sock to slow the boat’s drift. “This allows us to use a minimal amount of weight, and yet still keep the baits moving along on the bottom,” he explains.

** Lighten Up**

Tackle for San Diego bonefish is pretty light — usually 8- to 10-pound-test monofilament line on a 7-foot ­light-action spinning rod and matching reel. The biggest bonefish we catch is around two pounds, but as I fight my first San Diego bone, I marvel at its strength. It uncorks three blistering runs, and once it is close to the boat, Nelson warns me that the fight is far from over. He’s right. The fish continues to dive for the bottom with stamina that takes me around the boat twice before we put it in the net.

Yet even after that, I marvel at its strength. Just holding it for photos is difficult, a job made even tougher thanks to the fish’s copious coat of slime. During the spawning season — usually April and May — the Cortez bonefish get even slimier, but the action can also be spectacular. These are when Nelson’s 20-plus-fish days occur.

“The fish school-up during spawning season, and once you find them, the action can be nonstop,” says Nelson. “Still, you can catch them any time of year, and we release every single fish to help keep it that way.”

The next time someone mentions bonefish, watch his face when you tell him of the most unlikely yet ­productive destination for bones: San Diego Bay, home of West Coast chrome.

** San Diego Bonefish Tackle Box**

Nelson likes to use a Carolina rig with tungsten bullet weights that slide through eelgrass and shed weeds.

Weights range from 1⁄4- to 1⁄2-ounce, depending on the depth and speed of the drift, and Nelson puts a small bead between the sinker and swivel to help protect the knot. Leader length ranges from three to four feet. Nelson uses small, light hooks such as Gamakatsu’s size 4 Split Shot/Drop Shot hook or an equivalent hook size and style.

Threading the delicate ghost shrimp on the hook takes a bit of practice, but start by inserting the hook on top of the shrimp just in front of the tail, then inch the hook forward, and bringing the point out on top at the carapace. As a result, the bait drifts backward, as if kicking its tail to evade a predator.

Baits and Rigs: Live or frozen ghost shrimp

Rods: 7-foot light-action spinning rods

Reels: Light spinning reels such as Accurate SR-6 or Okuma Inspira 20

Line: 8- to 10-pound-test monofilament

Terminal Rig: 1⁄4- to 1⁄2-ounce tungsten bullet weight and bead on main line, swivel, and 4-foot, 8- to 10-pound mono leader, with a No. 4 Gamakatsu Split Shot/Drop Shot hook

** San Diego Trip Planner**

What: Cortez bonefish.

Where: Lower San Diego Bay south of the Sweetwater River. Focus on water ranging from five to 12 feet, fishing the edges of 20- to 30-foot depressions throughout the lower bay. For a list of area ramps, visit

When: Year-round, April to May for spawners.

Who: Private-boat anglers with reliable craft from 16 feet and up.

Here are guides who fish San Diego Bay, and can help you learn the most productive techniques:

1) Capt. James Nelson 619-395-0799

2) Capt. Bill Schaefer 858-277-8087

3) Capt. Barry Brightenburg 619-540-8944

Distant Cousins: Bonefish on the Left Coast are a little-known fishery but plenty sporty.
California Style: The San Diego version is known as the Cortez bonefish.
Drift Away: Strategy is to drift to find the depth where fish are feeding.
Use a Carolina rig with tungsten bullet weights that slide through eelgrass and shed weeds.
Ghost shrimp are a top bait for California bonefish. Use a “slurp gun” to suck up crabs from the mud.
Go Light: San Diego bones are well sized for light tackle.
This map of San Diego Bay shows the best areas to bonefish, along with nearby boat ramps.
Captain James Nelson uses a slurp gun to capture ghost shrimp – one of the best bait for San Diego bonefish.
The best place to find ghost shrimp is on mud flats at low tide.
San Diego bonefish don’t give up easy, despite their diminutive dimensions.
SWS West Coast Editor Jim Hendricks bows to give line to a Cortez bonefish hooked on light tackle.
Cortez bonefish are surprisingly strong, usually uncorking two or more blistering runs and then fighting hard closer to the boat.
SWS West Coast Editor Jim Hendricks battles a Cortez bonefish at boatside.
Cortez bonefish have beautiful coloration, which seems to change depending on the viewing angle.
Cortez bonefish in San Diego Bay grow to a maximum length of about 17 inches.
The bonefish in San Diego Bay have a heavy slime coat that gets thicker during spawning season – usually around April and May.
Nelson releases all bonefish to help sustain the population in San Diego Bay. Moving water across the fish’s gills help revive it prior to release.
While bonefish in San Diego don’t “tail” like those in the tropics, they are still fun to catch on light tackle. This one darts away from the boat.