As already mentioned, there is great beach fishing all along the So Cal coast, including public beaches right near the plant.
Most of the So Cal lake fishing will be bass and panfish at this time of the year since the water gets too warm for trout. Also, in most of the lakes that do still get trout will find the trout deep. One exception is Lake Cuyamaca in the mountains east of San Diego. It gets trout year round and is shallow. At about 4000ft altitude the water stays cool enough most of the summer.
Note that catch and release for trout is not allowed in most So Cal lakes while it is ok for other species. At Cuyamaca, all fish must be caught as this is necessary in this fishery.
There are a number of lakes in San Diego county that aren’t too far away from San Onofre. Lake Hodges southeast of Escondido has been great for bass, bluegill, and crappie lately as has Lake Sutherland outside of Ramona. Most of the lakes operated by the city of San Diego are only open three days a week. Hodges and Sutherland, though in north San Diego County are part of the city lake system. Information on the San Diego City Lakes can found here:
www.sandiego.gov/water/recreation/
Another north San Diego county lake of note is Lake Dixon, just north of Escondido. A potential world record largemouth bass was caught there a few years ago but it was foul hooked so it didn’t count. Info on Dixon Lake can be found here:
www.escondido.org/dixon-lake.aspx
Farther north and inland are Lakes Skinner, Parris , Elsinore, Hemet and Diamond Valley. Google will find you information on those lakes. I haven’t fished those as I have so much to choose from in San Diego County.
All of the local lakes have daily permit fees in addition to CA license requirements. Most of the lakes fish better from on the water, whether in a tube, kayak, or boat.
Small trout are available in some “local” mountains. These include the forks of the San Gabriel, Sespe Creek and Piru Creek. You will have to drive though high traffic areas to reach these waters.
Irvine Lake is a private lake near Irvine that is stocked with huge triploid trout. It also has bluegill, crappie, bass, and catfish. I think the current access fee is $22 but I believe you don't need a CA license. Its not known as a flyfishing destination and it can get crowded but some people to flyfish there. You can look it up at www.irvinelake.net
Also in the San Bernardino and Big Bear areas are Bear Creek and Deep Creek. The better areas require a lot of walking and sometimes some bushwhacking. Same for San Jacinto creek in San Jacinto state park.
Best consistent trout fishing is a few hours north to the Kern River drainage or up the Eastern Sierra between Lone Pine and Bridgeport.
Another option is to book a guide for some saltwater fishing on San Diego Bay our out on the Ocean. There are a number of guides working out of San Diego as well Orange County and Long Beach areas. Mako Shark trips out of San Diego are very popular. Bowman Bluewater Outfitters is the premier flyfishing for shark service in So Cal.
Nearest Fly Shop to San Clemente/San Onofre is His and Her’s Fly Fishing in Costa Mesa. Next nearest would be Bob Marriotts in Fullerton, then Bluewater Tackle/San Diego Fly shop in Solana Beach and Temecula, followed by Stroud Tackle and So Cal Fly Fishing Outfitters in San Diego.
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