Bay Area weather: Here's when rain and thunderstorms will arrive

The available storm energy forecast for Tuesday morning from the Bay Area to the Sierra Nevada. Thunderstorm cells that develop in the Sacramento Valley will have plenty of energy to work with in the morning hours. This could lead to a few rounds of thunder and lightning in parts of the Bay Area as isolated cells drift toward the coast.

Showers and isolated thunderstorms could drift into parts of the Bay Area Tuesday morning as the roller-coaster of June weather continues this week.

The National Weather service and several morning runs from the North American and high-res rapid refresh weather models are signaling around a 20% chance of thunderstorms in the Bay Area on Tuesday morning, down from the 45% chance issued on Monday's forecast.

That said, there is still plenty of energy in the air for isolated thunderstorms to develop on Tuesday.

A low-pressure system that began in Southern California kicked off a branch of thunderstorms around Big Sur on Monday afternoon. This same system will drive the next cluster of storms into the Bay Area on Tuesday morning.

Weather models signal a rush of showers from the Sacramento Valley into parts of the South Bay and Santa Cruz Mountains starting Monday after 10 p.m. These showers are likely to scatter, meaning some towns may get drenched in downpours while others stay bone dry. Some of these showers may also carry a charge, meaning brief flashes of lightning aren't out of the question for parts of the East Bay, South Bay and Santa Cruz Mountains.

The European weather model's outlook for available energy in the air over the Bay Area on Tuesday, with 90 to 130 joules per kilogram of energy expected for parts of San Francisco Bay and the Peninsula.

By Tuesday morning another band of showers and thunderstorms is expected to form in the Sacramento Valley that could contribute into more unsettled weather arriving in parts of the East Bay and Peninsula.

Most weather models signal a fair amount of convective available potential energy, also known as CAPE — a measure of how much energy the atmosphere can draw on to raise thunderstorms. Models forecast anywhere from 90 to 130 joules per kilogram of energy in the air over San Francisco Bay and the Sacramento Valley; these levels are close to that amount of energy that was available a couple of weeks ago when brief thunderstorms formed in Lake County.

Rumbles of thunder aren't out of the question for the Diablo Range and inland cities like Walnut Creek. Occasional lightning could also occur in San Francisco Bay as some of these thunderstorms ride the wave of energy toward the Peninsula.

There's also the risk of showers redeveloping in the Santa Cruz Mountains, though they may end up dying out quickly since most of the atmospheric energy is forecast to settle by the water. Any rain that does fall will only amount to a few hundredths of an inch to up to a tenth of an inch in a few isolated areas. That said, it's looking like Tuesday morning will be the most active weather period for the Bay Area.

Once the sun begins to break through the clouds around noon on Tuesday, expect most of the showers and thunderstorms to clear, with a few lingering showers in the Santa Cruz Mountains and some of the coastal hillsides. Calmer, sunnier conditions are then likely to return for nearly the entire Bay Area by sunset.

San Francisco: A few thunderheads might bubble up around the Embarcadero, Hunters Point and the Golden Gate Bridge on Tuesday morning, raising a chance for flashes of lightning mixed in with scattered showers just off the coast. The air over the city is going to feel more like a blend of winter and June Gloom by Tuesday afternoon as light rain and drizzle continue along the hillsides of Twin Peaks, Billy Goat Hill and Mount Davidson. That said, the warm, humid air overhead is likely to raise daytime highs to the mid-60s in downtown and most neighborhoods east of Sutro Tower, while lower 60s settle on the west side.

Rain clouds will gradually begin to clear Tuesday evening, while the usual ebb and flow of the marine layer kicks up after sunset. Look for some foggy conditions by the water overnight, with a slight chance of some fog coming ashore. Nighttime lows will generally hover around the mid-50s.

Pacific Coast and Peninsula: Motorists on the Highway 1, I-280 and Highway 101 corridors will want to watch for slippery conditions on the Tuesday morning commute. Rounds of light rain and isolated thunderstorms are on tap for the coastline, with most of the turbulent weather lasting through noon. Thankfully, most of the unsettled weather is set to stay just off the coast, which could make for an occasional light show on the western sky.

Mostly cloudy skies are likely to persist throughout Tuesday, with light rain and drizzle lingering along the Santa Cruz Mountains. Residents near San Andreas Lake, Emerald Hill and Portola Valley could hear thunder at times in the morning as leftover showers break apart on the foothills. Look for daytime highs in the lower 60s on the coast and San Bruno Gap, while Millbrae and communities east of the I-280 corridor can expect temperatures in the upper 60s. A few cities, like Menlo Park and Redwood City, could break 70 as warm, humid air sprinkles the Peninsula.

It's still June, and the marine layer looks to make a comeback starting Tuesday night. Weather models hint at coastal fog while mostly cloudy skies build over San Francisco International Airport. Expect nighttime lows in the mid-50s.

North Bay: Mostly cloudy skies with a mix of light showers are on tap for Marin, Sonoma, Napa and Solano counties on Tuesday morning. Some of these showers could spark lightning at times, with the highest chances of thunderstorms along the Mayacamas Mountains and off the coast of Sonoma.

Lingering showers are possible Tuesday afternoon in the highlands, but most weather models trend toward drier conditions. Sunshine will slowly return to the valleys, allowing daytime highs to reach the upper 60s in Napa, Santa Rosa and Petaluma. Residents in coastal Marin County will get a bit more of the usual ebb and flow of the marine breeze, keeping highs closer to 60 while the slightly warmer air over Solano County keeps delta cities like Benicia and Vallejo closer to the mid-60s.

Most weather models lean into the marine layer returning Tuesday night, meaning residents by the water can expect patchy fog starting just after sunset. Look for nighttime lows around the lower 50s.

East Bay: The scattered remains of showers from the Sacramento Valley are likely to spill into the San Ramon and Livermore valleys on Tuesday morning, which could lead to stray showers and a rumble of thunder or two in cities like Walnut Creek, Pleasanton and Dublin. The bulk of thunderstorm is looking to stay over the Diablo Range through noon, but the rumbles might be heard all the way in the east-facing sides of the Oakland and Berkeley hills. Light rain will be possible on the bay shore, raising concerns about slippery conditions along the I-80 and I-880 corridors.

Thankfully, most rain will clear out by Tuesday afternoon, with mostly cloudy skies slowly becoming sunnier through 6 p.m. Look for highs near 70 by the water — Richmond, Alameda and Hayward — while inland residents east of the Caldecott Tunnel can expect temperatures in the lower 70s. Marine layer clouds might resurface on the bay shore and delta after sunset, with weather models signaling a cool night with lows in the mid-50s.

South Bay and Santa Cruz: Rumbles of thunder are likely over the summits of the Santa Cruz Mountains on Tuesday morning. Showers are likely to peak just after dawn across Felton, Ben Lomond and Scotts Valley, while residents along Monterey Bay can expect a chance of scattered showers through 10 a.m.

Most of the unsettled weather will clear Tuesday afternoon, leaving mostly cloudy skies in the Santa Clara Valley and most of Santa Cruz County. Sunshine is likely to break through after 2 p.m., allowing daytime temperatures to reach the lower 70s in the inland valleys, mid-60s in the mountains and lower 60s along Monterey Bay.

The ebb and flow of the marine layer will allow patchy fog to return to parts of Highway 1 between Capitola and Santa Cruz after sunset, with nighttime lows likely in the mid-50s. Residents farther inland aren't as likely to get the marine air, but the scattering of warm air from earlier in the day will allow nighttime lows to stay above 50 degrees.

Reach Gerry Díaz: [email protected]; Twitter: @geravitywave