I have to admit...I wonder how consistently collected the data is, and to what extent varying local standards influence it. I certainly do have many fond memories of Lewes and Rehoboth - the Delmarva Peninsula is a much cooler and more unique place than most people realize (where else can you eat corn and crabs that came from the same farm?) - but best in the country? Really? The northern half of the state is on Delaware Bay, which is the mouth of the Delaware River, that drains between Pennsylvania and New Jersey through Philadelphia. And that's cleaner than Catalina, an island in the Pacific with strong currents and no nearby rivers (not to mention probably a stronger commitment to their environment)?
Looking at local data, Imperial Beach is a sadly unsurprising 1 out of 5 quality, with Coronado 3 out of 5; Mexico and TJ are clearly the culprit here, but they are consistently unable or uncaring about this problem. (Or in active denial; see this clever study that proved what we all knew.) But La Jolla shores came in at only 2 out of 5. The best rated beach in San Diego County was Moonlight in Encinitas at 4/5.
But I really don't know what to make of these ratings. In particular they don't correspond well with the Heal the Bay ratings for San Diego County beaches. These gave an A or B to all of them along the ocean except for Torrey Pines State Beach, which to be fair, does have a naturally sediment- and microbiota-rich canyon-draining marshland outlet right there. I emailed both organizations; we'll see if they can make sense of the gaps.
Added later: the NRDC responded at length explaining their ratings. The response is below.
The Heal the Bay Beach Report Card (BRC) is based on actual beach bacteria monitoring data provided and compiled by SD County Environmental Health. Our methodology has been vetted and endorsed by the CA State Water Resources Control Board as an effective way to communicate beach water quality to the public.
In the links you provided, it looks like the blogger is comparing the NRDC's annual summary to our weekly website grades. The grades on our website are based on the last 30 days of available monitoring data per location.
We also release an annual report (each year just before memorial day) that is based on one year of actual beach bacterial monitoring data. We include a summary of beach closures due to sewage spills but the grades are based solely on the actual bacteria data.
you can find our most recent annual report here: http://www.healthebay.org/sites/default/files/pdf/beachreportcard/BRC_2013_WEB.pdf
The San Diego section is on page 16 and 17, and the grading methodology is on page 74+75.
It is important to remember that these annual reports, and even our website grades that are based on the most recent data, do not indicate 'real-time' water quality. I usually suggest looking at a location's grade history to see if a beach generally scores A grades throughout the year (or if water quality fluctuates wildly throughout the year) if you really want to dig into whether a location is safe to swim.
you can see this historical grade info on our website by clicking the 'historical data' tab on the map balloon on this page (for example) http://brc.healthebay.org/?id=309&lat=32.9337&lng=-1
we also report beach bacterial advisories and closures due to sewage spills in as close to real-time as possible on our twitter account @beachreportcard