Much of the Bay Area was temporarily under a flood advisory Monday as heavy rainfall drenched the area during the biggest storm in months, with minor flooding reported in San Francisco, flash flooding threatening a recently scorched spot in Napa County and traffic incidents snarling the afternoon commute.

San Francisco residents encountered flooding on various streets as the city was cloaked in gray skies and soaked by downpours, according to multiple city agencies. In the late afternoon, a large puddle collected at Divisadero and Post streets, where drivers and even a runner splashed through the water.

Crews with San Francisco Public Works were hustling to clear storm drains as the agency received "a lot of reports of localized flooding due to drains blocked primarily by leaves," said Rachel Gordon, communications director.

The San Francisco Department of Emergency Management had received multiple reports of flooding shortly before 5 p.m., according to public relations officer Denny Machuca-Grebe. Flooded areas included Alemany Boulevard and the intersection of 17th and Folsom streets.

"We are working closely with our city partners to ensure the calls are routed to the right agency, and the hazard is mitigated," Machuca-Grebe said. "We will continue to monitor the storm so disruptions remain minimal."

The National Weather Service issued a flood advisory for San Francisco and parts of Alameda, Contra Costa, San Mateo and Santa Clara counties that remained in effect until 6:45 p.m., with the agency warning of minor flooding in low-lying and poor drainage areas due to excessive rainfall.

The San Francisco Fire Department had responded to roughly five reports of flooding as of 4:30 p.m., mostly isolated in the Diamond Heights and downtown areas, said Capt. Jonathan Baxter, the agency's spokesman.

He said firefighters had responded to reports of flooded streets and buildings on Diamond Street, Laguna Honda Boulevard, Bush Street and Lucky Street in the Mission, where they cleared clogged drains.

Baxter said the fire department recommended that residents stay home during the storm, and urged drivers out on roads to avoid entering puddles of water because they could be deeper than they seem.

Elsewhere in the Bay, the storm seemed to wreak havoc on the freeways. The California Highway Patrol incident feed documented dozens of collisions, roadway flooding and other reported hazards in Oakland, San Jose, Redwood City and Santa Rosa, including a flood reported on U.S. 101 south of Novato.

A possible tornado touched down around 4:30 p.m. near Pescardero in San Mateo County. The NWS will send a damage survey team to investigate on Tuesday.

The weather service also issued a flash flood warning Monday afternoon for the area surrounding the Pickett Fire burn scar in West-Central Napa County, warning of heavy rainfall and the potential for dangerous debris flows.

The alert, which was in effect through 5 p.m., covered the region from Pickett Road to Silverado Trail, including Simmons Canyon and nearby rural terrain.

The NWS said shortly before 5 p.m. that heavy rain had ended in Napa, although lighter rain could persist.

Radar and automated gauges detected between 0.5 and 0.7 inches of rainfall, with rates expected to increase to as much as 1 inch per hour, forecasters said.

For Napa County, "Flash flooding is ongoing or expected to begin shortly," the National Weather Service reported. "Excessive rainfall over the burn area will result in debris flow moving through the Simmons Canyon and areas near and between Pickett Road to Silverado Trail."

Officials warned that the steep, fire-scarred slopes left behind by this summer's Pickett Fire could quickly give way under intense rain, sending mud, rocks and vegetation cascading downhill.

The weather service described the hazard as "life-threatening flash flooding" and urged residents and motorists to stay clear of creeks, dry arroyos, and recently burned areas.

Affected locations include Dutch Henry Canyon Road, Swartz Creek Bridge at Athena Springs Road, and areas near Pond Outlet and Duvall Lake. Authorities said rockslides and mudslides were likely in steep terrain.

The Pickett Fire, which ignited on Aug. 21 and burned 6,819 acres, was declared fully contained on Sept. 7 after destroying five structures. Fire crews have since been conducting repair work and monitoring the area for lingering hazards.

Residents who observe flooding are urged to report it to local emergency services "when you can do so safely," officials said.

Chronicle meteorologist Greg Porter contributed to this report.

Heavy rainfall drenches Bay Area roads as flash flood alerts spread