San Diego Bay Fishing: a Kayak Perspective

One of my favorite things about living in San Diego is the accessibility of the fishing. In Oregon, getting to productive waters often involves long drives, multiple days off, and a considerable amount of planning. When you're driving five hours each way to get to a spot, it makes it difficult to really learn the area and get the most out of the fishing. You're usually happy to just catch anything. Even closer locales, such as those available along the northern Oregon Coast and even in downtown Portland, required you to at least make a day out of it. The only place that was close enough to my house to fish for only a few hours was the notorious Bethany Pond, a place that I will never, ever return to (but the reason for that is a different story). In addition, most fisheries were heavily seasonal and constrained by Oregon's unpredictable weather and even more unpredictable department of fish and wildlife. San Diego is different, with fish available 24/7, 365 days a year. This is almost entirely the result of San Diego Bay, and its smaller, manmade counterpart Mission Bay. Even the worst weather days allow you to fish the harbor, and unlike in Oregon harbors, a variety of gamefish can be easily found within them. In fact, fish can be found in nearly every part of each bay. Even though I've written a lot more about fishing La Jolla, over the years I've done way more bay fishing. While plenty of bay fishing articles by more experienced fishermen exist, I wanted to give my perspective.

Part 1: THE BAYS

San Diego Bay: San Diego Bay is large. Not nearly as large as San Francisco Bay, but I'd hardly call it small either. It's about 19 square miles, and fish can be found anywhere from where the mouth meets the ocean to the very end of the bay near the Mexico border. Much of the bay is used for military operations and is restricted (restricted as in they have guys with machine guns posted 24-7 ready to shoot anyone that gets too close), but most of the water is easily accessible and completely legal to fish. The layout and bathymetry of the bay drastically change from north to south. The north section of the bay is very industrial, rather narrow, and with deep channels that go up to the 60-80ft zone. Most of the harbors, military bases, and piers are in this section of the bay. This area can be extremely heavy in boat traffic. I do not recommend being anywhere near the main channel in a kayak during summer weekends, particularly in the late afternoon when offshore fishing boats are all racing back in. The offshore boats in particular are usually in a hurry, either to clean all the tuna they caught or to race back to the dock and forget about their skunk as quickly as possible. They will not slow down for you, will not change their course to avoid waking you, and it's safe to say that even if they managed to flip you, they wouldn't stop to check if you are okay. Even more dangerous are the "pleasure boaters" and the dreaded drunk jet skiiers. Some of them are legitimately villanous to kayakers, and I have had more than one particular occasion where a speedboater thought it would be funny to do donuts around me. Being primarily a kayaker, I usually fish areas that are a relatively close paddle to convenient launch areas and somewhat protected from the hustle and bustle of the main channel. Although there is excellent shore fishing as well, I prefer kayaking because any dedicated shore pounding in the bay quickly turns into a perpetual battle with the "YOU-CAN'T-FISH-HERE'S."

Anyone that fishes the bay is very familiar with the "YOU-CAN'T-FISH-HERE'S." These are people who, for whatever reason, seem to have a major issue with the existence of fishermen. They will stop at nothing to prevent you from fishing somewhere. I do understand some of the issues fishermen present. Some are very inconsiderate, and will trash an area with discarded line, leftover bait, and beer cans. However, this isn't everyone, and I don't think it justifies the attitudes I've gotten from some people that I've encountered while bay fishing. Much of this surrounds the issue of fishing private docks and marinas for Spotted Bay Bass, which to be fair is technically illegal. While most people don't care, all it takes is one paranoid boat owner or power-drunk dockmaster to ruin your day. This is where having a kayak or float tube has an advantage. Article 10, Section 4 of the California constitution dictates that as long as you aren't directly on anyone's private property, any body of navigable saltwater is for public use and no individual may claim ownership of it. This is to protect the public from Southern California's notorious wealthy coastal elite. I guarantee that if private beaches were possible in this state, there would be nowhere left for the public to go.

Despite what some may tell you, there is no "peripheral area" included in what is defined as private property. You can be in a kayak a foot away from a dock, and you're still not trespassing. Just remember: "Article 10, Section 4." That being said, every time I've told this to someone mad at me for fishing near their dock or boat it only made them angrier. It's safe to say that the people getting extremely worked up by someone fishing near their dock don't fall within the "reasonable people" category, unless you're being openly disrespectful by skipping lures against their hull or blasting loud music. As a result, it's crucial to always be respectful! That way, if someone is nevertheless taking issue with your presence you can rest assurred that it's their problem, not yours. At the end of the day, if someone is being ridiculously persistent, aggressive, and/or threatening to call the cops (they will undoubtedly embellish the situation at hand over the phone to make it worth the police's time to come over and investigate), you might as well just leave. There's always other spots to fish and I would prefer to not spend a day on the water dealing with this. I will never understand what makes some people see someone else quietly and respectfully fishing by themselves and immediately think "I need to put a stop to this."

This is why I love the south bay. Unlike the north bay, the south bay is far more remote, much wider, and much shallower. While it has less structure than the north bay, fewer boaters have a reason to go there and the numerous treacherous shoals and sandbars require those who do venture south to be a lot slower and more careful. Shore fishing is usually more laid back, and there's a lot more area to hit. Unfortunately, since the drop offs and structure are usually a lot shallower and further from shore, it's not as ideal for shore pounding. However, numerous species are more common in the south bay than the north. These include Bonito, Shortfin Corvina, Yellowfin Croaker, and Bonefish. The "YOU-CAN'T-FISH-HERE'S" are less common and less aggressive. "No fishing" signs are few and far between. The south bay recieves less pressure than the north, and its wide area allows a lot more fish to remain "hidden in plain sight," so to speak. I will go more into the species found in the bay later.

Mission Bay: Mission Bay is a lot smaller than San Diego bay, and interesting in that it is a manmade body of water that marine plants, invertebrates, fishes, birds, and mammals naturally colonized. Its small size and popularity with water sport enthusiasts can make it frustrating and even dangerous to fish during weekends and the summer (they have to start breathalyzing people before giving them the keys to a jet ski rental), but its accessibility can make it a great place to fish for a few hours during weekday mornings or at nighttime. The fishing is definitely tougher and harder to figure out than San Diego Bay, but the average quality across most different species seems to be better and this alone makes it a lot more rewarding. I love fishing Mission Bay during the nighttime, as it is extremely protected, has little boat traffic at night, and is overall a safer place to be alone at dark than its larger counterpart to the south. I live a lot closer to Mission Bay than the big bay, so it's a great place to go and kill a few hours whenever I get the itch to fish. My favorite San Diego tackle shop, Dana Landing, is right on the bay, and they even have skiff rentals and guided trips for sale.

Mission Bay has a lot less structure and variable bathymetry than San Diego Bay, and much of what is considered productive structure and cover is dominated by eelgrass. I never thought I needed a fishfinder for Mission Bay, but since I started bringing one my catch rates increased exponentially. Most of the time I'm not even finding fish with the fishfinder, only the tall, healthy eelgrass that Spotted Bay Bass in particular like to live in. While it's not as well known for "exotics" like Corvina and Bonefish as San Diego Bay, virtually any species found in the latter ecosystem can be found in Mission Bay as well. Mission Bay's small size makes it ideal for kayak fishing, and I greatly prefer kayaking the bay to shorepounding or renting a skiff. Shorepounding can be very good, but it is often very conditions/tide dependent (minus tides!) and certain parts of the bay are extremely shallow sandbars that can be an outright waste of time to fish from shore. When I started kayaking the bay, I began to quickly figure out why I would never catch fish from some areas, as I would be 25+yards from shore and still be in two feet of water with no eelgrass or similar cover. I never seem to do that well from the Dana Landing rental skiffs for some reason, but that's a personal problem.

Part 2: THE FISH

Spotted Bay Bass: Spotties are the mainstay of bay fishing here. If there were no Spotties, there would be a lot more slow days on the water. They're an eager to bite species that will hit nearly any kind of artificial lure, bite during the day and the night, and pull extremely hard for their size. What they lack is size, unfortunately. If they averaged 10lbs instead of 10 inches, the gear that you would need for bay fishing would be drastically different. In reality, if you were to catch a 4lb fish you would be a local hero for awhile. A 14" fish is considered a nice fish and also the minimum legal size, but they aren't considered good to eat and most do not take kindly to those who kill Spotties. They certainly are a fish that is worth more alive than dead. To catch them, people use almost everything imaginable. They hit live bait such as sardines and smelt, dead bait like shrimp and squid, and almost any bass lure except for topwater (even though they've been known to occasionally hit even these). Swimbaits, curly tail grubs, tube baits, shallow-diving hardbaits, crankbaits, texas rigged baits such as craws, underspins, flukes, dropshots, seriously almost anything. Spottie fishing seems to be more about creativity with lure choice than finding something that they will eat, but on some days they can get picky and require more finesse presentations. They love structure such as eelgrass, dock pilings, rip rap, rock piles, and drop offs. Moving water is important for getting lots of them to bite, but it's not necessary.

Barred Sand Bass: Sand Bass are like Spotties on steroids. They grow a lot bigger, and I also think they're the hardest pulling out of the three species of saltwater bass even for their size. They are more of a deeper water fish than Spotties, and while juveniles can be caught nearly anywhere the larger ones are more migratory and most common in the deep main channel of San Diego Bay. Like Spotties, they also like moving water and structure. The Sand Bass in the bay seem to be partial to biting at night, but they will bite during the day as well. They aren't picky about bait either, but since they live in deeper water and hug the bottom larger swimbaits and similar leadheads are the most popular baits for them. They pull extremely hard, so heavy bass gear, strong line, and tight drags are a must. I usually use straight 65lb braid when Sand Bass fishing at night, which also allows me to straighten most hooks when snagged before losing the lure. I used to insist on using fluorocarbon at night, but a buddy convinced me otherwise. Fluoro at nighttime is pointless and a waste of money. Sure, you get more abrasion resistance with fluoro if a fish buries you in structure, but with straight 65lb test they shouldn't even be able to reach the structure!

Calico Bass: While Calico Bass are more known for being a coastal kelp bed fish than a bay fish, they do reside within the rocky areas at the mouths of most bays. Some very large models hide in plain sight in these seemingly obvious spots, and it seems like these rock-dwelling bass are more heavily night-biters than those found in the kelp beds. They will eat just about anything a Spottie or Sand Bass eats (if anything, they might be even less picky), and since you're fishing for them in heavy structure it's extremely crucial to use strong line and pull as hard as you can. Pop em or stop em!

California Halibut: Halibut might be one of the most desirable, if not the most desirable sportfish in the bays. They are large, making them look impressive in "hero shots" (don't act like this doesn't matter to you), are tricky to consistently target, are great eating, and while they aren't the hardest pulling fish they do have a very unique fight responsible for lots of agonizing heartbreaks. While they don't have the initial pulling strength of a bass or the explosive stamina of a Yellowtail, they are very good at finding ways to no longer end up on the line and make you look foolish. I think it's because of their muscle structure and behavior. Unlike midwater swimming fishes, Halibut mostly lay on the bottom and are designed to go on short, powerful bursts of speed to ambush prey or escape predators. You can see it in their meat: the famous flaky, white meat of Halibut is comprised almost entirely of fast-twich muscle fibers that favor fast bursts of speed. They need to rest after each burst of energy, but recover fast. The classic way of losing a Halibut is to bring it to the surface, assume the fish is tired out, and attempt to net it right as it unleashes a crazy burst of energy and breaks the line on a last-ditch dive down to the bottom. It's almost like diffusing a bomb; one wrong move and it explodes. As a result, when fighting and landing a Halibut it's imperative to relax and take your time. They won't bury you in structure, they usually aren't hooked in areas infested with sea lions, and as long as you don't let its head break the surface they'll lay placidly alongside the boat for as long as you need to get the fish in the perfect position. Way more Halibut are lost by getting excited and jumping the gun than by waiting too long to get a good net or gaff shot. They can even swim backwards out of nets! While live bait is king for attracting their attention, they will eat dead bait and are eager biters of an assortment of lures. They often show up at unexpected times, and are the reason why I always bring a large net or gaff out with me no matter what species I'm targeting. I've caught legal halibut on tiny pieces of ghost shrimp on ultralight tackle, as well as swimbaits, hardbaits, dropshots, curly tail grubs, imitation shrimp, and dead sardines. The best way to guarantee a large Halibut seems to be using ultralight gear without a big enough net. The minimum size is 22".

Sharks, Rays, and Skates: While large pelagic sharks like Great Whites and Threshers are known to enter the bay, the resident Sharks and Rays that reside within the bays for extended periods of time are a lot less fearsome. The most common species are Leopard Sharks, Smoothhound Sharks, Horn Sharks, Bat Rays, Round Stingrays, Diamond Stingrays, Butterfly Rays, and Shovelnose Guitarfish. All can be caught by soaking dead baits such as mackerel, squid, tuna chunks, sardines, and honestly almost any other small fish. Freshness is more important than type. Leopard Sharks are the most popular, as they fight well on light tackle and are very handsome fish with a unique appearance. Smoothhounds are usually small, but are pretty cute and can also put up a decent fight on ultralight gear. Horn Sharks are not particularly common, and are more of an oddity than a gamefish. Bat Rays are well known for being extremely strong and the most likely bay culprit if anyone finds themselves spooled or has a rod dragged in. While they fight hard and have lots of endurance, their fight isn't particularly exciting as they usually just pull hard in one direction without too much urgency. Round Stingrays are a pest and the ones usually stepped on by swimmers and waders. Diamond Stingrays are the stingrays that would actually be bad to step on. Butterfly Rays are an interesting looking fish that resemble stealth fighters, and their inclination to hit lures often leads to some disappointment when that trophy Halibut turns out to be "just" a Butterfly Ray. However, they are great fighters. Shovelnose Guitarfish are unique looking fish with interesting behavior (their body shape allows them to swim in inches of water), and are supposedly very good eating but I've never been bothered to try one. They're certainly common enough where eating a few wouldn't be an issue, but seem like they would be a major hassle to clean.

Another shark of interest is the Angel Shark, a species that would have great potential as a sportfish if they weren't so rare. Unlike many other sharks which feed primarily by scent and prefer their bait to be natural, Angel Sharks are highly visual feeders that readily strike a wide variety of artificial lures. I've seen them caught by fly fishermen. While they don't fight very hard, they have a jaw-dropping strike and are capable of putting out a good run or two. In addition, they are FEARSOME to handle. Their placid, graceful appearance when in the water belies their enormous mouth of razor sharp teeth (there are videos on the internet of them swallowing smaller sharks whole), and they act like a large halibut crossed with a boa constrictor when you grab their tail. They will try to bite you, and bringing one in a kayak or float tube is a bad idea. If not in a decent sized boat with enough room to get away from the shark, I recommend beaching Angel Sharks if you are lucky enough to hook one.

Corvina: I have plenty to say about this cultish fishery, and the link to it can be found here: http://spooledkamranw.blogspot.com/2020/12/vampire-diaries.html

Bonefish: I also wrote an article about Bonefish to break my years-long blogging hiatus: http://spooledkamranw.blogspot.com/2020/12/look-whos-back.html

Croakers: Croakers are a lot of fun. The most common species in the bay is the Yellowfin Croaker, which is something like a mini redfish. They eagerly hit almost any bait or lure (including ones very large for their size), and fight very well for their size. Unfortunately, like most other fish whose fight is described as being good "for their size," they are rather small. They're decent eating but have a reputation for accumulating toxins easily and should be avoided in many parts of the bay, although it likely won't kill you or even make you sick. Although they're lots of fun on ultralight gear, the circumstances in which they're hooked is usually while targeting other species and they can be rather disappointing when you're hoping for a Corvina or Bonefish. Especially considering they pull harder than Corvina and their initial strike is similar to that of a Bone when using ultralight gear. They also closely resemble bonefish when you first see their silvery shape with Yellow fins at deep color in the murky water. A very underappreciated fish!

And with the humble Croaker, I conclude my thoughts concerning bay fishing in San Diego. I am not an expert bay fisherman by any means, but I have put a decent amount of time into them over the last few years. I figured that I would share some of my observations that can't be found in other bay fishing articles, especially my experiences with the "YOU-CAN'T-FISH-HERE'S." Growing up in a place where such consistent fishing opportunities aren't available, I am grateful to have the opportunity to live so close to such a diverse, accessible fishery. If you are an experienced bay fisherman, stop laughing at me! If you are a beginner, I wish you luck in your bay fishing endeavors and hope that you gained something from reading this article. Anyways, it's time to hop in the kayak and go fish some docks.