A rush-hour delay caused by flooded tracks at the Powell Street Station in San Francisco — in the middle of summer — points up a BART issue that doesn’t get nearly the attention that overcrowded trains, finicky air-conditioning and the seemingly daily “equipment problems” command: a steady supply of subterranean water.

Groundwater moving through downtown San Francisco’s sandy soil en route to the bay leaks into the subway between the Embarcadero and 16th Street Mission stations. It seeps through cracks and joints in the tunnel walls, creating a steady drip-drip-drip and even trickling like a mountain stream in places.

One of those places is the southwest end of the Powell Street Station. And that’s where a drain that funnels the water into the sewer system clogged with debris at just the wrong time, Monday evening’s rush hour.

Soon, water was pooling a foot deep on the eastbound trackway and rising rapidly toward the third rail. Since water and electricity don’t mix well, BART halted trains heading toward the East Bay outside the station about 5:45 p.m. while it sent workers in to unclog the drain.

The job was completed in about 15 minutes, without injury or damage. But until the drain was unplugged, the tracks to the East Bay were stopped up. Trains stretched back to the Daly City Station, and the platforms were packed.

“This is the first time I’ve heard of a train being delayed by flooding at Powell,” said Taylor Huckaby, a BART spokesman who has been with the transit system for two years. “It’s rare.”

Flooding might be rare, but the flow of groundwater into BART’s tunnels is pervasive — so much so that that maintenance crews refer to the area as “the rain forest” or “the Amazon.”

“I ride a lot and I see it here all the time,” Katy Conrad, 58, a compensation analyst from Walnut Creek, said Tuesday as a stream of water flowed into a drain on the tracks at Powell. “Sometimes I’ve even seen it coming down the walls.”

BART battles the intrusion by using sump pumps and drains and by caulking gaps in the tunnel walls. That’s usually sufficient to keep the floodwaters down.

Joel Pomerantz, a historian and self-described citizen scientist, has studied San Francisco’s subterranean waters and says the problem BART faces is common. Many downtown buildings and construction sites are forced to dewater the soil — the developer of the tilting Millennium Tower condo building at Second and Mission streets blames dewatering at the under-construction Transbay Transit Center next door for its troubles, something the public agencies that are building the transit hub dispute.

People sometimes describe the city as being home to underground creeks and springs, but most of the moisture is simply groundwater. The city’s hills soak up rainfall and runoff, and the water makes its way downhill toward the ocean to the west and the bay to the east.

This winter’s heavy rains pumped the hills fuller than usual, meaning bigger subsurface water flows that will last longer and at greater pressure, Pomerantz said.

“If there’s more water in the sponge of the ground, it’s going to create more water and it’s going to be coming out for a longer period,” he said.

The ground downtown is particularly sandy, and groundwater flows quickly there. Passengers standing near the southwest end of the Powell Street Station platform can sometimes hear what sounds like a waterfall, but Pomerantz said it’s really a pump extracting water from the soil and dumping it into the sewer.

Hoping to make the best of a damp situation, BART is working with the energy company NRG to install larger pumps to take the water from the Powell Street Station, turn it into steam and sell it to downtown building owners for heating or air-conditioning. Until that happens, the agency hopes that $570 million included in last year’s voter-approved Measure RR bond measure to pay for better tunnel waterproofing will prevent a repeat of Monday’s rush-hour flood.

Workers now inject caulk into joints in the tunnel lining to keep water out, Huckaby said, but it wears away quickly. BART plans to replace that with bentonite, a natural clay compound that’s long-lasting and should hold up better.

Pomerantz said a better solution would be to install a rubberized membrane or liner, using materials not available when BART was built in the 1960s, on the outside of the tunnel instead of injecting sealants from the inside. But that would require extensive, and expensive, construction that might not be worth the cost.

BART’s rain forest may be a hassle, Pomerantz said, but it can be controlled, and isn’t a hazard to passengers.

“I see no big dangers at all,” he said. “This just seems like a teachable moment to remind the citizenry of two things: first, that infrastructure needs maintenance on a regular basis, and secondly, that people are part of natural systems. There’s no way around it.”

Laurel Theren, 61, of Oakland, wasn’t caught in Monday’s flood delay, but it didn’t surprise her.

”It seems like it’s always here,” she said over the sound of the trickling water at Powell. “With BART, it’s always something.”

Michael Cabanatuan is a San Francisco Chronicle staff writer. Email: mcabanatuan@sfchronicle.com Twitter: @ctuan