From Scripps biological oceanographer Dr. Peter Franks:
RED TIDE: There's a reasonably dense red tide growing off Scripps Pier. It's been chugging along for a while, but it became visible (to me at least) yesterday. From what I can tell, one of the dominant species is Lingulodinium polyedrum, a bioluminescent dinoflagellate (in layman's terms, a little single cell with a flagellum that makes its own light). This means that we might have a nice light show tonight, and in subsequent days if the weather remains nice.
What's happening? The dinoflagellates have little bags of chemicals that mix when the cells are disturbed, creating a chemical flash of light.
Why wait until dark? The cells have a natural rhythm to their light production cycle - why make light when the sun's out? They will only make light (bioluminesce) when the sun has gone down.
Are they toxic? No. We tend not to get blooms of toxic phytoplankton here in the Southern California Bight.
How long will the bloom last? Depends on the weather. A few cloudy, windy days will tend to make the bloom dissipate. As long as the weather is sunny and calm, we could see the bloom for several weeks.
Why can't I see it in the water? The cells tend to migrate to the surface of the ocean around noon, and go back deeper in the water in the evening. Your best chance to see the red tide (it's actually brownish) is around noon.
Why do the organisms form bands parallel to shore? The cells can swim a bit, and interact with the flows of the water driven by other forcings. The bands of brown water are high concentrations of cells which have accumulated in the troughs of internal waves. These waves are like surface waves, but are much slower, and much larger in amplitude. If you sit and watch long enough (an hour), you should see the bands move with the waves (usually onshore). There are also patterns formed around Scripps Pier through interaction with the rip currents.
Here's what you can do: Get a clear glass jar or bottle and take a sample of the water from the beach (or as far offshore as a friendly neighborhood surfer will take one for you). Take it home, and put it in a cool, dark place (your bathroom would be ideal). After the sun has gone down, lock yourself in the bathroom or closet with the lights off, and give your eyes time to adjust to the darkness. Then give the bottle a swirl. With any luck, you'll see one of nature's most beautiful light shows.