It wasn’t just the moderate to heavy rainfall that soaked much of the Bay Area early Tuesday. It wasn’t only the increasing winds that rose past 60 mph in high places and blew consistently near 35 mph everywhere else.

It wasn’t just the forecast for thunderstorms or hail from the ever-thickening, ever-darker clouds that seemed to look angrier and angrier with each succeeding hour.

Taken together, all of it spoke to the arrival of the roughest system since the November downpours.

“This is one of those lousy storms that is wet, windy and nasty. But it’s definitely cold,” National Weather Service meteorologist Brian Garcia said late Tuesday morning. “That’s kind of the trademark of a Pineapple Express and atmospheric river. So that’s gonna bring a lot of moisture, and it’s going to keep coming.”

Garcia said the weather service was eyeballing the frontal boundary of the system before noon. It soaked the North Bay upon its arrival and was expected to do so even more in the afternoon.

At 1 p.m., the weather service had recorded a 24-hour rainfall total of 5 inches in Kentfield, 4¾ inches in San Rafael and 2.4 inches in Santa Rosa.

A bit more south, San Francisco received 2.3 inches in the 24 hours before 1 p.m. In the East Bay, Richmond had received 2 inches; downtown Oakland had received just shy of an inch; and Danville and Hayward each had received a half-inch.

In Santa Cruz County, the heaviest rain was atop Ben Lomond (2¾ inches) and in La Honda (2.1 inches). Los Gatos received about six-tenths of an inch to pace the Santa Clara County in the South Bay, while San Jose Mineta International Airport recorded barely more than one-tenth of an inch.

The system was poised “really to move inland” after noon, Garcia said.

“We’re waiting for the worst of it to set in,” he said. “Everything is going to increase here as we move into (the afternoon).”

That was likely to mean heightened winds inland. Near Marin County, the strongest gusts topped 70 mph before noon, according to the weather service. Atop Mount Diablo in the East Bay, 67 mph winds already had been recorded, and the weather service said they were expected to get more intense.

Also expected to increase was the unstable air. Garcia said the instability has been caused as the warmer air mass moves across the region trailed over the ocean by a colder one moving in to replace it. That instability made the thunderstorms, lightning and hail all possible, he said.

The weather service said a General Thunderstorm Outlook went into effect at 10 a.m. and was set to expire at 7 p.m.

“It’s going to be the immediate coastal area, but even farther inland out in the East Bay, the potential is there,” Garcia said.

Following a dry day today, the cold air mass is expected to bring more rain on Thursday, according to forecasters. A longer dry stretch is set to follow that one, and the weather service said it’s needed to settle things down.

“We’re going to have a lot of water on the ground with this system,” Garcia said. “By the time we get to Thursday, the soil is going to be saturated. So any rain that falls is gonna probably going to become runoff pretty quick. It won’t take much to cause some flooding.”

Flooding already was a concern Tuesday. The weather service issued a flood warning for areas of the Russian River near Guerneville, and a flood watch for the region that started Monday remained in effect until 4 a.m. today.

Rain has been falling off and on in the region since last Friday, the first measurable rain outside the North Bay since Jan. 3.