Fishing San Diego Bay – Tips & Tricks

  • Updated
  • 17 mins read

Fishing San Diego Bay – Tips & Tricks

The quality of fish in Mission Bay is very good and, while it’s fun to fish, it isn’t always easy. But that’s just a big part of its appeal, of course. This is an amazing article that will help you catch fish in SD bay

The original post was written by @DJ Thrillz.

The fishing in SD Bay is simply amazing.

You basically have a buffet of fish to target 365 days out of the year, morning or night, rain or shine.
San Diego Bay fishes completely different than Mission Bay does. It’s bigger, deeper, and a little bit of wind can have a huge impact on the fishing, which can be good, or bad. It’s definitely structured different. In MB you have weedbeds, small drop offs, some docks and bridges, and that’s just about it. In SD Bay, there are shoals, giant holes, docks, big drop offs, flats, piers, bridges, and areas with rip rap that fish tend to hang around. Options are endless, and possibilities are endless. No matter what you target, you will not know what’s on the end of your line until you see it.

For the most part, almost all of us target spotted bay bass. We all know they will eat anything… Well, if you didn’t now you do! So let’s start there. 


You can find spotties all over SD Bay. I’ve caught them in just about a foot of water, to as deep as 50′. As mentioned, they eat just about anything, but the most cost effective way to catch them is with plastics. You will catch more spotties on plastics than any other species our bay has to offer. I prefer 3″-5″ baits for fishing 1′-20′ of water. I’m a shore based angler for the most part so unless I’m fishing by the Midway where it easily hits 30’+ at times, I’m fishing under 15′ of water.

The absolute hog spotties of SD Bay hide either in places you aren’t able to fish, places that are hard to get to, or places where people yell at you to leave because they think they own the water. All other areas hold 6″-13″ spotties on the regular.
If you just want to catch spotties from shore, you can go anywhere on Shelter Island, Harbor Island, Liberty Station, Tidelands Park, Glorietta Bay, J St, Pepper Park, Spanish Landing, Ferry Landing, Crown Cove, Fiddlers Cove, Seaport Village, Embarcadero Park, and Coronado Golf Course. That’s right, you can park your car in their parking lot, walk along the cart path only, and access the waters edge to wet a line. It’s kind of a bit of trouble just to catch a few small bass, but I’m just putting the info out there for you to take in.

From a boat or yak, you have a gazillion places you can go. For quantity, the South Bay(south of the Coronado Bridge) holds a ton of spotties. The square mile flats is one of my favorite areas to fish, you have the potential of a 50+ fish outing! There is a nice population of spotties on either side of the base as well, but be prepared to get rushed by the little grey boats with the 50 Cals if you get too close for their liking. Some chunky spotties at their docks on the north side of the base in Glorietta Bay, but you have to time it right to get a decent amount of fishing time in over there. The south side of the base is also great for bass, but it’s only great at higher tides. Just be careful of the little island that becomes almost invisible on super high tides. A bit south of that little island is Fiddler’s Cove, which holds quite a few smallish fish. To the east of that, is the Sweetwater Channel and Pepper Park. Just around the corner to the north of that channel is an area dubbed “The Elbow”, which I came to know well thanks to Ed Surek. Many bass have flown over the rails there. It’s always my first stop when launching from Pepper Park…

Further south, Crown Cove and the Coronado Cays always has plenty of bass to offer. When I am down that far south, it’s rarely for bass though.

In the North Bay, the moored boats off of Tidelands Park pretty much always hand out some tally marks. Ignore the Sea Hag if she’s outside yelling at you for “being on her lawn”. If you happen to rent a skiff from Seaforth Boat Rentals(Glorietta Bay), you wont need to travel too far to find all the action in the world.

All of those spots in the yellow have produced multiple 30+ fish outings, and I usually share this map with those who are having trouble catching fish in SD Bay, or who are traveling to SD Bay to get on some fish.
For those of you who have your own boats, this is probably my favorite area for bass from a boat in SD Bay.

From the bridge, and in the middle of the channel, is really good when the drift is just right. You can literally pick fish off on almost every cast from the bridge all the way past the Midway at times. You can almost make the same drift in more shallow water but you’d have to start near the Ferry Landing. Having a fish finder and making waypoints is a must so that you can start in the same area. On the other side of the channel but in the same area, these areas marked in yellow along the Embarcadero have put out some great numbers as well.

On a vessel I prefer outgoing tides since I’ve done better on those tides. No real explanation, just my experience.
A bit more north and to the west is the northeast end of North Island. That place hands out plenty of bass too. Not too far from that are the moored boats at Shelter Island, they always produce! Always! If you can’t catch a bass there, take up a new hobby! The western end of Harbor Island is one of my favorite areas to catch spotties from the rocks. Areas in yellow are for spotties, and in the orange is spotties and especially halis. Don’t tell anyone…

Up between the sub base and the bait barge is a killer area to fish, problem is the navy likes to think they own it. So they chase you out 99% of the time. Lastly the Zuniga Jetty has a good amount of bass there, mostly calicos but spotties in the mix. If you like sand bass, the colder months are your friend, and so is the main channel from the mouth to the bait barge. Larger white curltails have rewarded me with several larger Sandies. Gotta go big, and fish deep. From shore, during the same months, up and down the Embarcadero between Laurel Street and G Street pier have given me some decent ones up to 19″. Caught the bigger ones with Gulp 4″ swimming mullets in camo off G Street pier, back when they didn’t care if you fished from it. 10#-14# set up around all that structure.

As always, greens, browns, and oranges produces better for me while targeting spotties. Black at night!
An 8#-10# set up is the norm from shore, and I’d bump it up to 12#-20# for drift fishing.

1. Liberty Station
2. Spanish Landing
3. Harbor Island
4. America’s Cup Harbor
5. Shelter Island
6. Kellogg Beach
7. Sub Base
8. Zuniga Jetty
9. Navy Fishing Pier
10. Embarcadero(ranges from the Coast Guard Station all the way to Embarcadero Park South)
11. The Midway
12. G Street Pier
13. Seaport Village
14. Embarcadero Park North
15. Embarcadero Park South (Embarcadero Pier)
16. Coronado Ferry Landing Pier
17. Tidelands Park
18. Glorietta Bay
19. Square Mile Flats
20. Fiddlers Cove
21. Crown Cove
22. Coronado Cays
23. The Elbow
24. Sweetwater Channel
25. Pepper Park
26. J Street Marina(J St. Pier)
27. Power Plant (even though it no longer exists, I will always refer to this location as Power Plant)

There are halibut all over SD Bay. For bigger ones, live bait is a must and drifting around the sub base(if you can) and then again around the northeastern end of North Island is usually a lock. The main channel from the Embarcadero Pier to the Midway has a history of producing nice ones as well.
From shore, I favor Harbor Island, the shoals at both ends of Shelter Island, Liberty Station, and the no fishing area next to the Fish Market by the Midway. Plenty of luck on flatties at each of those areas. Shallow diving cranks(Luckycraft, Megabait, Rapala, etc.) that resemble a smelt, sardine, or grunion have proven themselves. For plastics, dropshotting is a hell of a method for them. 5″ flukes in white, 4″ basstrix in smelt or sardine, and larger curltails in natural colors can’t go wrong. 12#-25# set up is about the normal for boaters while 10#-15# is the normal for shore based fishermen.

Croaker can be found throughout SD Bay all year long, mainly yellowfin croaker. YFC are pretty much spread around SD Bay. You can find loads of them just about anywhere in the South Bay, all around Coronado golf course throughout Glorietta Bay, Tidelands Park, Harbor Island, and Liberty Station. Spotfin croaker are somewhat rare in SD Bay now but can be caught from time to time. Last I heard of them being caught was in Liberty Station in the mid 2000’s. Black croaker(china croaker) are all over Pepper Park, behind Shelter Island, and Seaport Village(North Embarcadero Park). Croaker will hit plastics from time to time but ghost shrimp, razor clams, and mussel will get them much more frequently.

Bonefish are a hell of a fun species to target. The South Bay has a bunch of them. Focus on the flats down south near the Cays and outside Crown Cove. The square mile flats hold them too. Some of the bigger bonefish I’ve heard of being caught were in Glorietta Bay. Liberty Station and Pepper Park have a bunch as well. Best months to target them are May-August. They love small grubs, and will hit swimbaits from time to time. But drifting a live ghost shrimp(2″-3.5″) on a C-Rig with 4#-6# line is the best way to target them IMO.

Leopard sharks and big bat rays are common in SD Bay. These are best targets from a boat, but harder to handle. Harder to target from the shore, but easier to handle. This is why I target them in MB instead, but if you must target them in SD Bay, you’ll want about a 40#-50# setup with an 8/0 circle hook. Better have the most freshest and bloodiest mackerel for the best shot at hooking a nice one. Fish Mack’s whole if they are smallish, fillets or big steak chunks if they are larger. I’ve always had the best luck with the heads. You will want some water movement regardless of where you fish for them. If you go deep make sure to use plenty of weight to cover depth and current. Chumming doesn’t do much good when going deep, but works wonders when fishing more shallow. Plenty of larger Leo’s and rays down south, then again in the main channel outside the bait barge all the way down to Shelter Island.

Shortfin Corvina are a popular target in our waters. Especially since the “big reveal” that they were not juvenile white seabass 15 years ago, and that they are yummy and can be kept at any size. Unfortunately they are now over targeted and over kept, and finding any pushing 30″ is just rare now. Hell finding any in the 20″ is like striking gold now. They are a fragile fish that need to be handled with special care. If you can use barbless hooks, and try to release them while still in the water their chance of survival is great. Put your hands all over them, drag them up the sand and you might as well fire up the grill. It’s an unfortunate thing, something so fun to catch being so fragile. Smaller ones are easier to handle and survive with no problem. Larger ones tire out and are slower to get going once released even if they were handled with all the care in the world. I will not give out any spots for them as I’m a bit passionate about them. But I will ask if you target them to just be careful with them. Use barbless hooks to help things out. If they get away so what, try again. Safest release anyhow. Low light to no light, March through October, shallow diving cranks or topwater lures. 10#-12# set up. That’s all the info I’m giving up on vinas. If you want to pick my brain in private I am willing to do that, just drop by any Shore Pounders event and come chat it up.

Bonito frequent SD Bay. Lots of them down in South Bay around Crown Cove, J street, and Fiddlers Cove. I’ve seen them all over by the base in Glorietta bay chasing bait, Tidelands, Ferry Landing, Embarcadero, and they really get active by Shelter Island pier. March-May, and again around August-October have a series of showings. From a pier, the bubble and feather method works great. My favorite way is with krocodiles in green Mack, blue Mack, and chrome with an orange strip. They love live bait, before anything else. 8#-10# is enough for them.

Barracuda start showing up around February in a couple places. Spanish Landing is one of them. Glorietta Bay, and Embarcadero Park South seem to be popular for them also. They keep pretty active throughout the grunion runs and simmer down in the Fall. 8#-10# set up.

Sargo, to be honest, is a great fighting fish. If they were as easy to target as spotties, I’d give two craps less about targeting spotties. There’s a nice population of them in the South Bay and again in Liberty Station. They absolutely murder live ghost shrimp, and will pounce on a 3″ swimbait if it’s in front of them. Once they reach 10″ they become fun. And if you’re lucky enough to catch one 16″ or bigger, you will stop thinking of spotties for a while. If I could pick one species to catch for the rest of my life and no other, it would be the sargo.
Those are some, not all, of the most frequently targeted fish in SD Bay.

Now a little about some of my experiences…. I will start with Harbor Island, since I have spent the most time on foot there in the entire bay. I will divide the island into two, right side and left side. When you are driving up to the street light you go one way or the other. The right side is by far the best side to be on. Up by the park area across from the Hilton is probably the most active area on the entire island. I have caught my biggest (SD Bay)bass there, and the most halibut compared to anywhere else I’ve targeted them. From the left end of the park(facing the open water) all the way to Tom Hamms Lighthouse is a great place to be in the Summer and Fall. As far as the left side goes, it is slightly deeper than the right side, and you can catch anything over there. I usually only hit the left side if the right side is packed with people. There is only one spot I like to fish from on the left side, a certain rock about two dozen footsteps down from the first set of parking slots. Memories…
There is a drain pipe right in the middle of the island near the traffic light, it gets pretty decent from there also.

If…… If you happen to know someone who can let you on the docks in the corner behind the Sheraton hotel, those docks will not let you down. Used to tube them, but it was a long kick from the beach at Spanish Landing and too much for my knees. The few times I hit those docks I was impressed. Lots of legals over there.
If you dare fish at either end you will most likely get a visit from Harbor Police. They’re kind of anal about fishermen on their property.

Fishing from shore down in the South Bay is kind of tough, but there is one particular area I like going to this time of year. That would be Crown Cove, early mornings during higher tides. You can fish for almost anything there, but the bonito usually make a showing, vinas, bass, Hali’s, and even bonefish will keep you busy. Only other time I’ll go to this area is at the beginning of spring.

The Wall at the Ferry Landing is a popular place to catch fish. Summer nights over there can be rewarding if you time it just right. It can get crowded there since a lot of people are there waiting for the grunion to rush the sand just north and south of the wall, but the chance of nice vinas and Hali’s is great.

The area by the old Power Plant….. pretty active when the tide fills in. Great tubing spot. You may even see a turtle or two….

Midway…. If you want a quantity over quality kind of day, the Midway has your back. I know that since I have stopped frequenting the Embarcadero, there have been numerous no fishing signs posted all over the place. If I am not mistaking, there are no fishing signs across the parking lot on the opposite side south of the Midway, which used to be a great area to fish as well. But in front of the Midway is still ok to fish as far as I know. Fish the stern of the ship for shallow water and big numbers, the side of the ship for deep water and meteocre numbers, or if you got a hair up your aZz fish next to the Fish Market casting back west. Nice little shelf there that holds a ton of bass and plenty of Hali’s.
Seaport Village can be decent, on the marina side. It’s somewhat deep and gives up good numbers. Gotta pay for parking. Matter of fact SD Bay has pay meters more places now than ever before, and I’m sure they’re not going to stop installing them anytime soon. So keep some spare change in your car just in case.

I mentioned this in the MB write up, and I’ll mention it again here-
Logging your outings is the number one tip I could give anyone. I’ve went through many tanks of gas roaming our waters, and keeping track of all the fish I caught, baits I used, and jotting down notes about the sessions. Not only my sessions, but I made notes of whoever is fishing with me and how they did too.
Staying mobile is the second best tip I can give. Roaming is how I ended up finding out most of what I know. It’s definitely how I found my favorite spots. Fish don’t normally come knocking on your door, you gotta find them. Although I gave a few general spots away, nothing beats discovering decent spots on your own. Plus, some spots I fished before are horrible now. Times change, fish move around. It’s not always going to be fireworks, so accept your skunk days in a positive way. Learn something from them, even if it’s “not to go there again” kind of lesson.

If this little write up helps a single person, then it was worth the time to type it up. I’m sure there are things I have left out, so I may add to it.


Best of luck to all of you!

Leave a Reply