Until 2003, there did not exist any national protocols in Mexico to determine the quality of ocean water used for recreation. In 2003, the Mexican secretariats of the Navy, Environment, Tourism and Health established a “Clean Beaches Program,” to evaluate water quality and establish a means to achieve a better environmental quality for Mexican beaches.

With the Clean Beaches Program, the government of Mexico began monitoring the water quality at various tourist beaches throughout the country, and issues reports on the findings. In Baja California, 21 beaches are monitored in the cities of Tijuana, Playas de Rosarito, Ensenada and San Felipe.

Recreating in waters with increased bacteria concentrations has been associated with increased risks to human health, such as stomach flu, nausea, skin rashes, eye infections and respiratory illness. However, to determine which beaches are fit, Mexico did not set the bar very high. Mexico’s federal environmental protection agency, Secretaría de Medio Ambiente y Recursos Naturales (SEMARNAT), considers a beach polluted if tests show the water exceeds 500 enterococcus fecal bacteria per 100 milliliters. Mexico’s federal health agency, Comisión Federal para la Protección Contra Riesgos Sanitarios (COFEPRIS), considers a beach polluted if tests show the water exceeds 200. The World Health Organization (WHO) considers a beach polluted if it exceeds 137 enterococcus per 100 milliliters.

Calfornia’s standards, which were established by AB411, classify a beach as polluted if the average count exceeds 35 enterococcus per 100 milliliters over a 30-day test period!

Greenpeace reports that the main reason for the unhealthy beaches of Mexico is that Mexico discharges 33,000 gallons of untreated sewage into the ocean each second. Only 40.2% of Mexico’s wastewater is treated before being dumped.

A COFEPRIS report on Mexican beaches for 2010 shows that of the 21 Baja California beaches tested, 17 exceeded the US standard during at least one test in 2010. All of the beaches tested in Tijuana, Rosarito and San Felipe failed at least once during 2010. One beach in San Felipe, showed a whopping 631 enterococcus per 100 milliliters, 18 times US federal clean water standards.

There is a continuing problem with raw sewage water flowing into the ocean in San Felipe. Authorities suspect that septic cleaning services which pump out septic tanks are clandestinely dumping the wastewater into the arroyos, which flow into the ocean. The Comisión Estatal de Servicios Públicos de Mexicali (CESPM), which operates San Felipe's sewage treatment plant, reports they only receive 30 tanker truck loads of effluent per day, which is far less than the amount of sewage generated in San Felipe.

California’s Heal the Bay, a non-profit environmental organization, monitors the health of 483 beaches in California, 77 of which are in San Diego County. 95% of San Diego beaches receive a grade of A or B from Heal the Bay. In fact, only one beach exposed to the Pacific Ocean received a failing grade. That was the beach at the outflow of the Tijuana River which carries runoff from Mexico.

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