Rainwater runoff from downtown sidewalks and suburban gardens dumps more toxic chemicals into San Francisco Bay than the large rivers that drain vast tracts of farmland in the Central Valley, according to a new study.

City dwellers are also responsible for one of the newest scourges in the bay - the ubiquitous plastic shopping bag.

In its annual report card on the bay, the San Francisco Estuary Institute found that heavy loads of mercury and PCBs are flowing into San Francisco, San Pablo and Suisun bays through the web of culverts and creeks that carry storm water from residential and industrial areas around the nine-county region.

Ten years ago, scientists believed that California's two largest rivers, the Sacramento and San Joaquin - which funnel most agricultural runoff from the Central Valley to the delta and San Francisco Bay - were the primary culprits.

But more advanced testing techniques show cities are the key source, according to Jay Davis, senior environmental scientist at the San Francisco Estuary Institute in Oakland. The volume of mercury flushed from the Central Valley may be half what had been estimated a decade ago.

"Historically, we thought (the Sacramento and San Joaquin) were the dominant inputs of contaminants in the bay, but our thinking has shifted," Davis said. "The tributaries from the urban landscapes are contributing more."

Higher levels of mercury are of particular concern, because when ingested by people and animals the heavy metal can cause a host of physical problems, including neurological damage. Tests of striped bass from the bay, a so-called "indicator species," show mercury levels at an average of 0.4 parts per million in 2009, Davis said, well above the 0.2 parts per million level considered safe for moderate consumption.

One of most mercury-laden waterways in the region remains the Guadalupe River, which flows from the Santa Cruz Mountains and the site of the now-defunct New Almaden Quicksilver Mining District, one of the largest historic mercury mining operations in North America. Various local agencies have partnered with one another with the intention of cutting mercury levels in the Guadalupe, from controlling erosion along river banks to adding oxygen to local reservoirs. That process helps prevent mercury from converting to methylmercury, the chemical form most frequently eaten by and concentrated in fish.

Efforts are also under way to slash the most visible types of contamination: cigarette butts, Styrofoam packaging and plastic bags. Last year, the San Francisco Bay Regional Water Quality Control Board approved a measure requiring municipalities in Alameda, Contra Costa, San Mateo and Santa Clara and Solano counties to reduce the amount of trash in storm water runoff 40 percent by 2014.

"Without a question, trash has become one of our highest priority water quality concerns," said Tom Mumley, assistant executive officer at the water board. "It affects the creeks, the shoreline and contributes to ocean pollution. The public simply has to create less trash, and cities need to capture more of it."