More than a million devout Hindus bathed in the Ganges River on one day during the recent Kumbha Mela festival, braving the risk of terrorist attack, stampede and petty crime for the chance to wash away the sins of a lifetime and open the gateway to heaven after death.

But perhaps the greatest threat to the devotees who flocked to Haridwar, India was the water itself.

The river is intensely polluted with sewage and industrial waste. Water-treatment facilities have been unable to keep up with India’s rapid growth, often held back by a shortage of funds and other resources.

A dip in the Ganges River in India is believed by devotees to wash away all sins. But increasingly it has become heavily polluted with sewage and industrial waste. Now, a $4 billion government program aims to clean the river.

Now, the spiritually cleansing waters of the Ganges are about to get some cleaning of their own. The Indian government has embarked on a $4 billion campaign to ensure that by 2020 no untreated municipal sewage or industrial runoff enters the 1,560-mile river.

Only 31% of municipal sewage in India undergoes treatment, according to the Central Pollution Control Board, a government agency in New Delhi, while the rest gets discharged into the country’s rivers, ponds, land and seas, contaminating underground and surface waters. More than 500,000 of the 10.3 million deaths in India in 2004 resulted from waterborne diseases, according to the most recent comprehensive mortality data from the World Health Organization.

The filth in the Ganges holds special resonance for this majority-Hindu nation. The Ganges basin supports more than 400 million of India’s 1.1 billion people, the majority of whom are Hindus, who revere the river as “mother” and “goddess.”

The cleanup initiative, which is supported by the World Bank, includes the expansion of traditional treatment facilities and, for the first time in India, the introduction of innovative river-cleaning methods.

Veer Bhadra Mishra, a 70-year-old priest and hydraulics engineer in Varanasi, the holy city downstream from Haridwar, has been a prominent advocate of treatment methods used abroad but not yet in India. His plan: to introduce a system to divert sewage and effluents, before they enter the river, to a series of specially designed ponds, for treatment and ultimately to be used use in irrigation or directed back into the river.

His efforts were mired in court and by opposition from local bureaucrats. The bureaucrats had a “difference of opinion” with Mr. Mishra about the best way to clean the river, says Ramesh Singh, general manager of Ganga Pollution Control Unit, the local government body charged with running government treatment facilities in Varanasi.

Mr. Singh says the technologies already in use were time-tested and reliable, but suffered from a lack of trained manpower and proper infrastructure, and a shortage of funds for equipment maintenance.

Last summer, after Prime Minister Manmohan Singh identified cleaning up the river as a national priority, the government in New Delhi increased funding to operate and maintain conventional treatment facilities, and also approved Mr. Mishra’s plan—giving $184,000 to his organization, the Sankat Mochan Foundation, for the design of a new sewage treatment plant.

The foundation is working with GO2 Water Inc., a Berkeley, Calif., wastewater-technology company. In the plan, 10.5 million gallons of sewage a day—13% of the daily output from Varanasi’s 1.5 million people—will be intercepted daily at the riverbank, and diverted. In a nearby village, water will pass through a series of ponds, where sunlight, gravity, bacteria and microalgae will clean the water. A larger pond system is planned, to process 33% more of the city’s sewage.

Devout Hindus come from all over to cleanse themselves in the Ganges for the festival of Kumbh Mela, celebrated every three years. The government has started a massive campaign to clean up the polluted river itself.

The treatment system “will be the best solution for dealing with huge amount of domestic sewage being discharged into Gangaji and other rivers in India,” Mr. Mishra said, using the honorific “ji” with the river’s local name, Ganga.

In Haridwar, the National Botanical Research Institute is developing a wetland with local species of reeds to absorb the polluting elements from the wastewater, according to U.N. Rai, a scientist heading the project. Other wetlands will be developed in other areas “to ease the current pollution load in the river,” Mr. Rai says.

The load is heavy. On a recent winter morning in Varanasi, lab technician Gopal Pandey descended the stone stairs of Tulsi Ghat, one of the holy city’s 84 bathing platforms, to fetch some Ganges water for testing at the Sankat Mochan Foundation, an organization run by Mr. Mishra.

In the laboratory, Mr. Pandey found that each 100 milliliters of the river’s waters were laden with 29,000 fecal coliform bacteria, which potentially cause disease. India says a maximum of 500 per 100 milliliters is safe for bathing in the river. Another sample from downstream, after the Ganges meets a tributary carrying a black mass of thick industrial effluents, showed 10 million bacteria—mostly E-coli—in the same amount of river water. Mr. Pandey’s verdict: “The pollution is at very, very dangerous level.”