It was drizzling lightly in late October when the midnight shift started at the Owls Head Water Pollution Control Plant, where much of the sewage in the New York City borough of Brooklyn is treated.

A few miles away, people were walking home without umbrellas from late dinners. But at Owls Head, a swimming pool’s worth of sewage and wastewater was soon rushing in every second.Warning horns began to blare. A little after 1 a.m., with a harder rain falling, Owls Head reached its capacity and workers started shutting the intake gates.

That caused a rising tide throughout Brooklyn’s sewers, and untreated feces and industrial waste started spilling fromemergency relief valves intoUpper NewYork Bay and the Gowanus Canal.

‘‘It happens anytime you get a hard rainfall,’’ said Bob Connaughton, one the plant’s engineers. ‘‘Sometimes all it takes is 20 minutes of rain, and you’ve got overflows across Brooklyn.’’ One goal of the U.S. Clean Water Act of 1972 was to upgrade the country’s sewer systems, many of them built over a century ago, to handle growing populations and increasing runoff of rainwater and waste. During the 1970s and 1980s, Congress distributed more than $60 billion to cities to make sure that what goes into toilets, industrial drains and street grates would not endanger human health.

But despite those upgrades, many sewer systems are still frequently overwhelmed, according to a New York Times analysis of environmental data.

As a result, sewage is spilling into waterways.

In the last three years, more than 9,400 of the 25,000 sewage systems in the United States—including those in major cities—have reported violating the law by dumping untreated or partly treated human waste, chemicals and other hazardous materials into rivers and lakes and elsewhere, according to data from state environmental agencies and the U.S. Environmental Protection Agency.

But fewer than one in five sewage systems that broke the law were ever fined or otherwise sanctioned by state or U.S.

regulators, the Times analysis shows.

It is not clear whether the sewage systems that have not reported such dumping are doing any better, because data on overflows and spillage are often incomplete.

As cities have grown rapidly across the United States, many have neglected infrastructure projects and paved over green spaces that once absorbed rainwater.

That has contributed to sewage backups into more than 400,000 basements and spills into thousands of streets, according to data collected by state and U.S. officials. Sometimes, waste has overflowed just upstream from drinking-water intake points or near public beaches.

There is no national record-keeping of how many illnesses are caused by sewage spills. But academic research suggests that as many as 20 million Americans each year become ill from drinking water containing bacteria and other pathogens that are often spread by untreated waste.

A 2007 study published in the journal Pediatrics, focusing on one Milwaukee hospital, indicated that the number of children suffering fromserious diarrhea rose whenever local sewers overflowed.

Another study, published in 2008 in the Archives of Environmental and Occupational Health, estimated that as many as four million people become sick each year in California fromswimming in waters containing the kind of pollution often linked to untreated sewage.

Around New York, samples collected at dozens of beaches or piers have detected the types of bacteria and other pollutants tied to sewage overflows.

Though the city’s drinking water comes from upstate reservoirs, environmentalists say untreated excrement and other waste in the city’s waterways pose serious health risks.

‘‘After the storm, the sewage flowed down the street faster than we could move out of the way and filled my house with over a foot of muck,’’ said Laura Serrano, whose home on Long Island, New York, was damaged in 2005 by a sewer overflow that filled it with waste about 12 inches, or 30 centimeters, deep.

Ms. Serrano, who says she contracted viral meningitis because of exposure to the sewage, has filed suit against Suffolk County, which operates the sewer system.

The county’s lawyer disputes responsibility for the damage and injuries.

‘‘I had to move out, and no one will buy my house because the sewage was absorbed into the walls,’’ Ms. Serrano said. ‘‘I can still smell it sometimes.’’ When a sewage system overflows or a treatment plant dumps untreated waste, it is often breaking the law.

Sewage systems are the most frequent violators of the U.S. Clean Water Act.

More than a third of all sewer systems — including those in San Diego, Houston, Philadelphia and San Francisco — have violated environmental laws since 2006, according to a Times analysis of Environmental Protection Agency data.

Thousands of other sewage systems operated by smaller cities, colleges, mobile home parks and companies have also broken the law. But few of the violators are ever punished.

The agency said in a statement that officials agreed that overflows posed a ‘‘significant environmental and human health problem, and significantly reducing or eliminating such overflows has been a priority for E.P.A. enforcement since the mid-1990s.’’ In the last year, agency settlements with sewer systems in the Hampton Roads area of Virginia and the east San Francisco Bay Area have led to more than $200 million spent on new systems to reduce pollution, the agency said. In October, the agency’s administrator, Lisa P. Jackson, said she was overhauling howthe Clean Water Act is enforced.

But widespread problems still remain.

‘‘The E.P.A. would rather look the other way than crack down on cities, since punishing municipalities can cause political problems,’’ said Craig Michaels of Riverkeeper, an environmental advocacy group. ‘‘But without enforcement and fines, this problem will never end.’’ Plant operators and regulators, for their part, say that fines would simply divert money from stretched budgets and that they are doing the best they can with aging systems and overwhelmed pipes.

NewYork, for example, was one of the first major cities to build a large sewer system, starting construction in 1849.

Many of those pipes — constructed of brick and ceramic tiles — are still used.

Today, the city’s 7,400 miles, or 11,900 kilometers, of sewer pipes operate almost entirely by gravity, unlike in other cities that use large pumps.