Fly Fishing Mission Bay

It’s summer time and the living is easy! My hometown of San Diego is the perfect summer vacation town, and it’s well known for this. We are extremely family friendly with miles of easily accessible sand beaches, good surf for body boarders and surfers, the world-famous San Diego Zoo, Legoland, SeaWorld, excellent restaurant with the best Mexican food outside of Mexico. About the only thing San Diego is missing is a NFL team, but that’s a bit of a sore topic.


Fly fishermen lined up on the shore
A Group of Fly Anglers Enjoying a morning on Mission Bay

San Diego is known in the bass world as a great bass fishery, but it’s not known for great fly fishing. We are a hidden gem, as we chase a variety of species within our city boarders and most of them will readily take a fly. Since we are a family destination, if you find yourself out in America’s finest city, don’t leave your fly rod at home.

One of my favorite local fisheries is Mission Bay. The reason this is my favorite and where I spend most of my time when I’m not chasing trout, it is easily accessible, no special gear is required to fish it, and there’s a variety of species that will eat a fly. Fishing times revolve around the tides, so it’s a great place to hit up for a couple of hours and then you can get back to your day. Sneaking away for a few hours on family vacation is a lot easier sell than a full day float trip.

The Bay

Mission Bay map
Mission Bay with fishing spots in red

Mission Bay is a man-made bay and is the largest man-made aquatic park in the country. There are miles of wade friendly sandy beaches. The image above shows some of my favorite fishing areas, that can be accessed by foot and offer great fishing.

The Gear

Fly Rods – 5-8 weights I fish a 6 weight Scott S4 and a 10’ 7 weight Redington PredatorRedington Predator fly rod

Fly Line – Matched to weight of the rod. A standard floating line will work fine. Floating with an intermediate tip or a full intermediate line also work well.

Rio saltwater line

Tippet: Rio Fluroflex Saltwater Tippet 8-12 pound test.
Rio Fluroflex Saltwater Tippet

Flies: Umpqua Deceiver Fly – White and Chart Size 2
umpqua deceiver fly

Umpqua Schmidts Reefer Mantis Fly Size 4

Umpqua Skinny Water Minnow Size 4

Umpqua Crazy Charlie Size 4 or Size 6, Tan or Pink

Umpqua Veveka’s Ghost Shrimp

Collection of bay flies
Hand tied bay flies

Wading gear: Wet wading is the norm, but you want to wear foot protection, as it is a public beach and not everyone respects the land. Orvis Christmas Island bootie is perfectly suited for this application. Waders and boats work during the colder months, but if your boots have any metal on or in them (including studs) you’ll want to rinse them along with all your fishing gear, as salt water is rough on gear.


Fresh caught halibut with a fly in its mouth
A nice Halibut taken on an Umpqua Deceiver Fly

Now that all the gear has been sorted time to hit the water. The most important factor for success is knowing the tides and currents. We want to fish during times of water movement, as this brings food to the fish and tells the fish it’s time to feed. A good rule of thumb is that an hour before and after high or low tide. There are a variety of tide apps available for smart phones, and my personal favorites are “My Tide Times” and “Tide Aware” and they are free on the app store.


Holding a bay bass
Jalen’s first fish on the bay, a nice spotted bay bass

Tapered leaders aren’t needed, as the fish aren’t spooky and don’t need to perfectly turn over a fly to cruising bonefish. Tippet of 6-8’ long that is looped to the flyline is my preferred set up. I use a non-slip mono knot for connecting the fly to the leader. The extra fly movement, I think helps with enticing fish to eat.


Holding a bonefish
My fiancé, Lesley, with a Cortez bonefish

Once you’ve found your spot and are rigged up, cast out into the bay, 30-50’ and let the fly sink. I will give it 10- 30 seconds and start stripping in. The stripping pattern is three (3) 12” strips and then a second or two pause, then repeat. They will hit on the pause more often than not, so be ready for a quick strip set and fish on! The fish live in and around the eel grass, so if you’re not getting some eel grass on your fly, let it sink longer until you do. The idea is to make a couple of fan casts, then move down the beach. The fish move around, so it’s important to keep moving to find them.


Yellow fin croaker
A fat yellow fin croaker

The most common catch in the bay is Spotted Bay Bass (Spottie). These fish are everywhere and hit hard and fight well above their size. They have strong head shakes, and a strong steady pull. They don’t peel off line, but they put up a fun fight. There’s also Sand bass and Calico bass that take up residence in the bay.


Don holding a spottie
Don with his first spottie on the fly!

Other catches are Halibut, Yellow fin croaker, Corbina, Spot Fin Croaker, Cortez bonefish, bonito, Corvina, shovel Nose guitar fish and an assortment of rays. There’s no real way to target a single species, since they all call the aby home, and they all eat the same style of flies. The unknown is another fun thing about fishing the bay, you never know what’s on the line until you land it.


Holding a small San Bass
Me with a miniature San Bass
Kevin holding a shovel nose guitar fish
Kevin with a really nice shovel nose guitar fish

The bay will definitely test your gear, so you want to make sure your knots and gear are in shape. I have a mate who hooked into something big (probably a ray) and took him to his backing and his backing to fly line nail knot failed and he watched his $80 fly line disappear into the deep. As much as this sucks for his pocket book, it sucks more for the fish that has to trail a fly line until the hook rusts out. It’s a good chance to make sure all your knots are up to the task.


Bat ray
Fly eating bat ray

Hope this gets you to try getting a bit salty with your fly game when you visit beautiful San Diego. If you are going to be in town, feel free to DM me on instagram with any questions and if I’m available, I’d love to come fish with you!


Nick holding a small fish
Nick with his first fish on the fly – They all can’t be monsters!
Fresh caught halibut
A legal 22″ Halibut that was released to fight another day!