EPA website on the 301(h) waiver was apparently last updated in 1994.
www.epa.gov/OWOW/oceans/discharges/301list.html

The following are listed as current "waiver" holders under Sect. 301(h):

Maine:
Bayville, Boothbay Harbor, Bucksport, Eastport, Eastport/Quoddy,
Jonesport, Lubec, Milbridge, Newton Highlands (Squirrel Isl.),
North Haven, Northport Village (Belfast), Searsport, Wintersport

"...Maine is a predominantly rural state, and relies heavily on decentralized sewage disposal facilities..."

Mass.:
Glouchester, Gosnold

New Hampshire:
Portsmouth

California:
Goleta, Morro Bay,
Orange County (San Diego, exemption to the filing deadline)

Hawaii:
Sand Isl. and Honouliuli (Honolulu)

American Samoa:
Fafuna (Pago Pago) and Utulei

Guam:
Agana, Agat and Northern Dist. (Dededo) Palau (Koror) Trust Territory

Alaska:
Anchorage,
Haines, Ketchikan, Pelican, Petersburg, Sitka, Skagway, Whittier, Wrangell

 
15,088 discharge districts do NOT have a waiver. Orange County is the biggest, by far,dwarfing all others except San Diego, which has the excuse of treating Tijuana's sewage.
"Secondary is not a perfect system", it's the first, minimum step.
HISTORY OF THE WAIVER: "EPA received 208 301(h) waiver applications... 45 applicants and permittees remain, including 36 waiver recipients and 9 applicants with decisions pending..."
"The majority of 301(h) waiver recipients are small ... discharge less than 5 million gallons per day (MGD)... the flows from these ... represent only 4 percent of the 620 MGD of wastewater under the 301(h) program..."
Orange County Sanitation District uses 240MGD, dwarfing the majority of the other dischargers, which are mostly located outside the continental US. Our "mass loading" of fecal solids is 20,000 metric tons per year, twice that of San Diego!
"...Less than half of the [waiver] 45 applicants/permittees are located within the continental United States...".
The waiver was intended for places, such as Anchorage, where the "good bugs" and digestion might die of cold, and where the population (253,000) is about what OC was before 1960... or else in places like Palau, which not too many reading this can even place on a map, or even on which side of Ocean.
Secondary treatment is NOT full treatment -- it is the MINIMAL LEVEL of treatment considered acceptable for protection of the public health.
The Orange County Health Care Agency and the Regional Water Quality Control Board (RWQCB) allows OCSD to monitor itself. This means researchers get continued employment only if they do not find the outfall to be a problem. Instead, perhaps researchers should be paid only if they find problems.
This is not a new issue. In 1985, Dr. Jack Skinner predicted that the sewage would come back to shore. In 1987, there was proof, which OCSD now claims they did not make public because they perceived "no interest" in the public over the issue.
If this study had been made generally available, would the 1988 waiver application have been granted? Possibly NOT, which might explain why it was not trumpeted about.
According to OCSD, "...looking back... we should have made it more public..." instead of allegedly attaching this important study, validating Dr. Skinner, to some buried annual report in 1992.

Puerto Rico does not like their waiver

EPA Abuse of Section 301(h) of the Clean Water Act Impacting Communities and Coastal Ecosystem of Puerto Rico Sra. Sarah Peisch Centro de Acción Ambiental, Inc. "Communities and environmental organizations in Puerto Rico denounce the U. S. EPA for discrimination against Puerto Rico in their negligence of enforcing compliance to the United States Clean Water Act legislation..."

California sewage dumping

San Diego: South Bay Ocean Outfall (SBOO)
  The South Bay Ocean Outfall receives 25mgd of advanced primary effluent from the International Wastewater Treatment Plant (Treating Tijuana's sewage from the TJ river). This partially treated water is discharged about 3 miles out, in 90 feet of water. There is no thermocline most of the year, and a visible plume at the surface. There have been coliform standards exceedences at recreational kelp beds just offshore. Surfrider has sued the federal government over this outfall, as has the state.

There is currently also a reclamation plant (City of SD, who co-owns the outfall with the federal gov't) that can treat up to 15mgd to tertiary that will be coming online any day now. Since there isn't enough market for the reclaimed water, it will be treated to secondary and comingled with the 25mgd from the IWTP before discharge out the SBOO.
(Info thanks to San Diego Ocean monitors, source on
request)