Live Anchovies
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Live anchovies are the best bait when fishing Southern California's lagoons. They can typically be found at area bait shops near the water. Anglers also can invest in a throw net, and catch their own bait if they find a school of anchovies.
Once you have live anchovies, get a bait sled to keep them living and at the ready whether fishing from shore or boat. This floating bucket is ideal for keeping the prize bait lively.
To fish anchovies, rig the hook through the nose of the fish and pair it with a sliding sinker. The sinker should be positioned above a swivel 2 feet above the hook. The sinker should be heavy enough to make the minnow sink slowly, yet light enough so it can still swim around. If live anchovies are not available, fresh dead or frozen anchovies will do, but don't expect as many bites.
Worms and Shrimp
Lagoon and back bay fish will take ghost shrimp, sand crabs, blood worms and mussels. Ghost shrimp, mussels and blood worms fished off the bottom are a good call in rocky areas and wide open flats, while sand crabs will turn heads in sandy shallows.
Smaller hooks in the 4 to 1/0 size range will work with these baits. Ghost shrimp are found as live bait and can be fished on a larger hook. Blood worms are alive, but fished as cutbait on smaller hooks. Mussels are cracked, and pieces of meat are fished on small hooks. Sand crabs are fished whole, so pick a comparable hook.
All of these offerings are fished best on or near the bottom. Add heavy weight when fishing with a tide flow or try a light sinker when tides are stable. Fish tend to eat when the tide is moving in our out. So check your tide tables before heading out.
Plastics Offer Alternative
If live bait isn't available and you are not into cut bait, try an alternative. Rig up a plastic bait, and spend time covering more water. Plastic baits like swimbaits, and hula grubs are ideal imitations of minnows and other creatures found in these waters.
One particular swimbait that works well is the chartreuse AA Worms Single Tail Shrimp. Thrown on a light-weight jighead, this deadly bait swims slowly over structure grabbing the attention of fish in the area. Spotted bay bass are traditionally found on the bottom, so casting the swimbait tight to docks and then swimming it back is a good way to entice strikes.
Another option is a creature bait like the Yamamoto Double Tail Hula Grub in green pumpkin with black flake. This bait is best rigged on a lightweight jighead. Sink this offering on a slow drop off docks and pilings or any other structure. Slowly swim the bait back to shore after it hits bottom.