Fly Fishing for Bonefish on San Diego Bay

Text and images by Craig Smith

Bonefish in San Diego Bay? Yes, they prowl the waters of the Big Bay as well as Mission Bay.  Visitors from outside Southern California are often surprised to learn about our Souther California bonefish because they think of species as a tropical fish. Folks from other parts of the country who learn that there are bonefish in San Diego Bay wonder if is worth coming to San Diego to target them.

Angler with a winter bonefish caught fly fishing in San Diego Bay
Angler with a winter bonefish caught fly fishing in San Diego Bay

The bonefish in San Diego bay is a subspecies called the Cortez Bonefish (albula gilberti) and has evolved to be at home in more temperate waters than its tropical cousins. They look very simlar to their tropical cousins. One distinguishing feature is the yellowish or orangish pectoral and anal fins, a coloration that is most prominent when backlit.  These fish also sport the blueish olive back and barring pattern of their cousins around the world though that coloration often fades upon removal from the water. Though they have been recorded as far north as San Francisco Bay, the Cortez Bonefish is primarily found from Southern California and down the coast of Baja California as well as the west coast of mainland Mexico as far south as Mazatlan.  San Diego Bay likely has the largest population in Southern California though we hear of occasional catches in Mission Bay as well as farther north in Newport Bay.

The local bonefish tend to be caught most often around eelgrass beds as well as sandy and muddy bottoms. Common local wisdom is that the southern areas of San Diego Bay are the best areas to catch bonefish. However, we have caught them near the surface in the deepwater shipping channels and in the kelp forests off Point Loma and La Jolla, near Zuniga jetty, in the surf, and throughout the entirety of San Diego Bay. We have caught them chasing small baitfish just below the surface and bouncing jigs off the bottom in 30 feet of water.  But most of our catches have come in water from 4 to 15 feet in depth over eel grass.  We do not find these fish tailing in very shallow water in the manner of tropical flats bonefish, so sight fishing is not an option worth pursuing.

Ghost shrimp are a significant food source for bonefish as well as other shrimp species, shellfish, crabs, marine worms, and small baitfish.  The most successful method by far for catching bonefish is to use whole or cut pieces fresh ghost shrimp as bait (if you are interested in using bait for bonefish in San Diego Bay check out this helpful article from Salt Water Sportsman magazine).  But we have also caught them with spinning and level wind  bait casting gear rigged up with plastic curl tail grubs on jig heads, plastic swimbaits, spinner baits, metal spoons, and hard bodied crank baits.  And of course, we catch them with flies too.

Typical San Diego Bay Bonefish
Typical San Diego Bay Bonefish

As noted above, the best way to catch bonefish in San Diego Bay is using live or dead bait of some sort.  If you can find a school of fish — they often move around quickly — it is possible to catch a dozen or more in a couple of hours.  However, when fishing artificial offerings, catch rates trend toward much lower numbers.  In 30 years of fly fishing San Diego bay the most bonefish I have caught in a typical four to five hour outing is seven. I know a handful of anglers who have caught more than that on the fly in one day. I have also gone months of fishing one to two sessions a week without catching one.   A few years back I had one three year stretch without catching one although I shared the boat with partners who did catch some during that period while I was fishing with them.   Unless specifically targeting bonefish with natural bait, most anglers consider bonefish an incidental catch when fishing the bay with artificial lures or flies.  Over time you will catch orders of magnitude more spotted bay bass, shortfin corvina, yellowfin croaker, halibut, mackerel, and other species than bonefish.

Angler with a San Diego Bay Bonefish.
This angler fishes San Diego Bay around 100 days a year: more chances = more bonefish

So what is the best way to go about catching bonefish on the fly in San Diego Bay?  To start, go fishing. Frequently.  Fish eelgrass and mud flats in 4 to 12 feet of water. Spend a lot of time in the south bay but don’t ignore outer areas of the bay.  Though I know one angler who has caught a few from the shore on the sandy beach on Shelter Island you really need some type of watercraft such as a boat, kayak, or stand up paddle board to improve your chances of success.   Find large expanses of mostly flat bottom areas and drift over them with the current and wind just as fish you would when targeting spotted bay bass.  You can find these areas with nautical charts.  If you want to narrow down some areas, then try to work sections near where the flats drop off into deeper channels.  Many species in the bay feed primarily when there is tidal current but bonefish do not seem to follow this pattern. So if you are hunting bonefish you do not need to plan your outing around the tides.

For a fly fishing outfit, a 5, 6, 7, or 8wt rod with a quality reel is suitable. Quality doesn’t need to be expensive.  You don’t need higher end gear since these fish are not going to stress your rod and reel. A reel like the Redington Crosswater is sufficient.  You will want to keep your fly near the bottom most of the time. Depending on the depth of the water you are fishing an intermediate line, a line that sinks at 3 inches per second (IPS) and a line that sinks at 6 IPS will cover the depth of water that will be most productive and the currents that you may find.  The 3 IPS and 6 IPS is just a rough guide.  Other sink rates will work as long as you can get to the bottom in the current.  As with targeting other species in the bay a selection of lines with three sink rates will get you in the zone in a wide range of conditions.  An intermediate sinking line may work fine in 8 feet of water with little current, but a line that sinks at 6 IPS may be needed in the same spot at peak current.  Your leader can be as simple as a level section 6 to 9 feet long of 8, 10 or 12 pound test nylon or fluorocarbon monofilament. You can use a tapered fly fishing leader if you prefer. The fish are not leader shy. One hundred yards of backing is much more than you will ever need.

Flies for San Diego Bay Bonefish
Examples of flies for San Diego Bay Bonefish

A wide variety of flies work.  I have caught more bonefish on size 6 and size 4 Clouser Minnows of various color combinations than all other patterns combined.  But that is because I fish Clouser Minnows more than all other patterns combined.  Other patterns to consider include crab and shrimp imitations,  traditional flats bonefish patterns, small streamers, spoon/wobbler patterns, and just about anything that looks like it might be food.  Our local bonefish really are not that picky when it comes to choosing meals.  If in doubt, pick flies that have orange, pink, olive, or chartreuse incorporated into their color scheme.  During the winter when large numbers of small baitfish congregate consider small, translucent streamers.

When you hook up a bonefish you can usually tell right away that you have not connected with a bass, barracuda, halibut or shortfin corvina, all of which often start the battle with a few head shakes.  When I hook up with something that doesn’t start with a few head shakes I immediately think bonefish or croaker (either yellowfin or spotfin) and even then I am often not sure what I have until I get a visual confirmation.  Both bonefish and croaker will often start by moving to one side or the other much more rapidly than a bass and will try to take some line.  The bonefish in the bay tend to dig to the bottom in a very determined fashion and change directions quickly in my experience.   Some anglers talk of long screaming runs but this is not my experience.  Sometimes short screaming runs — maybe.  Certainly nothing like catching bonefish on a tropical flat. In 30 year of catching bonefish in the bay I have had exactly one get into my backing and that fish was foul hooked in the dorsal fin.  I tend to put a lot of pressure on the fish immediately, even with 8 pound test leader and keep the fight near the boat. I rarely give more the 20 feet of line, and often give no line. I typically only fight the fish from the reel if I hooked it at the beginning of the retrieve shortly after the cast.  Often, if I take all pressure off the fish, it will simply stop running.

A fly rod caught San Diego Bay Bonefish comes to the boat
A fly rod caught San Diego Bay Cortez Bonefish (albula gilberti) comes to the boat

Bringing a bonefish to hand to release can be a tricky experience.  I always fish with barbless hooks and ideally I can grab the leader within a foot of the fish and as the fish shakes its head the hook pops out.  If it doesn’t pop out then I slide my hand down and try to grab the fly and rotate it out without grabbing the fish though this can be tricky if the fish is shaking its head.  Bonefish are pretty slimy and difficult to grasp and grasping them around the middle and over their lateral line can send them into a frenzy.  If I cannot release without grabbing the fish I may try a soft rubber net if I have one handy (having net on board a watercraft when fishing saltwater is a requirement in California).  Otherwise I will wait until the fish tires a bit more and slide my wet hand under the belly and lightly grasp the fish, then remove the fly with the other hand.  It helps to have a dry rag handy to remove any slime from your hand and/or sun gloves.

Cortez Bonefish from San Diego Bay - image shows the yellow fins
Cortez Bonefish from San Diego Bay - note the yellow fins

Eve though we do have bonefish in San Diego, I wouldn’t recommend our local waters to anyone as a destination to head to for the species.  But they are a fun catch that adds a bit of spice to the variety of fish in the bay.  They don’t make the long runs of a tropical flats bonefish but they do fight hard and on a typical day where you might catch a bunch of spotted bay bass if you get even a single bonefish that will be the catch most anglers will call the highlight of their day.