California's high-speed rail system may be more than a decade away from completion, but the beleaguered project is already casting a shadow over Palo Alto's plans to separate its streets from its rail tracks.

Specifically, it may make it practically impossible for the city to dig a train trench in south Palo Alto, near the Meadow Drive and Charleston Road rail crossings. This part of the rail corridor is among the sites that Caltrain is exploring for a future four-track segment, according to a new analysis that Caltrain staff and consultants shared with the city this week.

A trench, once built, would be very difficult to widen once the need arises to accommodate high-speed rail and expanded Caltrain service.

Caltrain's new analysis of four-track segments adds a fresh complication to the city's convoluted and meandering quest to select preferred alternatives for grade separations (the redesign of the railroad corridor so that roads and tracks would no longer intersect). The Palo Alto City Council has spent the past decade evaluating alternatives for its rail crossings, gradually narrowing down its options from more than 35 to about half dozen.

In south Palo Alto, where the council hopes to start construction, the trench alternative is one of three under consideration. The other two involve an underpass for cars and a "hybrid" design that combines lower roads and elevated tracks.

Even though the trench alternative comes with an estimated price tag between $800 million and $950 million and would involve pumping out and redirecting two natural creeks, city officials have been reluctant to abandon it. Compared to other alternatives, the trench has been politically popular because it would move trains out of sight and obviates the need to construct elevated structures.

If Caltrain picks south Palo Alto as its preferred location for a four-track segment, the alternative would become even less feasible because the trench would need to be significantly wider and more expensive. Caltrain is also evaluating two other parts of Palo Alto for a four-track segment: the area around the downtown transit station and the area around California Avenue, the new plans show.

"Ultimately, we will need one segment to advance," Edgar Torres, Caltrain's consultant from the firm Kimley Horn, told the council's Rail Committee during a Nov. 21 public hearing.

Today, Caltrain has just two four-track segments, at the Bayshore station on the border of San Francisco and Brisbane and at the Lawrence station in Sunnyvale. But as the transit agency prepares to increase service on its newly electrified corridor, it is looking to build more four-track sections so that express trains can easily pass local trains at various points along the corridor.

In addition, Caltrain is preparing for high-speed rail, a system that was approved by California voters in 2008 but that remains hobbled by rising costs and flagging political support. Under an agreement between Caltrain and the California High Speed Rail Authority, which funded the electrification of the rail corridor, the Caltrain board isn't allowed to make any modifications to the corridor that would preclude or make materially more complicated the future implementation of high-speed rail, Torres said.

Locations where Caltrain is looking to build four-track segments include Millbrae, the Hayward Park and Hillsdale area in San Mateo, and Redwood City. According to Caltrain's presentation, these areas could accommodate a "moderate growth" scenario with eight Caltrain trains and four high-speed trains per hour in each direction.

Caltrain is also exploring additional locations for its "higher growth" scenario, which calls for 12 Caltrain trains and four high-speed trains per hour. Under this scenario, at least one four-track segment would have to be in north Santa Clara County to meet Caltrain's operational objectives, according to agency staff. That's where Palo Alto comes in.

As the council's Rail Committee learned during its Nov. 21 meeting, each Palo Alto option would involve uncomfortable tradeoffs and steep challenges. In north Palo Alto, expanding the corridor from two tracks to four would force Caltrain to contend with the historic San Francisquito Creek bridge and the El Palo Alto tree, obstacles that the agency would rather avoid, Torres said.

If Caltrain opts to build additional tracks near the California Avenue station, the train corridor would intrude into Peers Park and require property acquisitions in the northern part of this segment. More critically, Caltrain would have to partially reconstruct the Oregon Expressway underpass, which cannot currently accommodate four tracks.

"There likely will be infrastructure modifications to the Oregon Expressway interchange to be able to accommodate four tracks at the Cal Avenue station," Torres said.

The south Palo Alto option also has its flaws. Centered around the San Antonio station, near the Mountain View border, it would require reconstruction of the San Antonio overpass. Specifically, the thick columns that currently support the road as it goes over Alma Street would need to be moved to accommodate the additional tracks.

"If the tracks were to be constructed at grade, it would mean a complete reconstruction of the interchange to be able to accommodate that," Torres said.

The four-track analysis could determine which grade separation options Caltrain ultimately supports. Jill Gibson, a consultant with Kimley Horn, told the council's Rail Committee that the information in the new report "will be used up and down the corridor to provide the city the guidance to be able to implement grade separation projects."

The information comes at a time when the council is feeling increasing pressure to choose its preferred alternative. Palo Alto recently landed two grants for grade separation: a $6 million grant from the Federal Railroad Administration for design work on all three segments and a $23.8 million grant from the California State Transportation Agency for work on grade separation at Churchill Avenue.

To get the funding, however, the city has to pick its alternatives by spring 2024, Chief Transportation Official Philip Kamhi told council members in August.

Council member Pat Burt, who chairs the Rail Committee, said the city will have to merge the new information it has received about the four-track segments with its ongoing analysis to meet its "aggressive timeline" for choosing its alternatives. The need for four tracks, he noted, could make some of the options that are currently on the table less feasible.

"The cost increase for one alternative going to four tracks may be a higher proportionate increase than another alternative," Burt said.

Trenches could prove particularly problematic. Caltrain staff and Kamhi all noted that if the city opts to move ahead with the trench, it would have to basically design it as a four-track project. This would be a significant departure from the two-track trench that Palo Alto and its consulting firm, Aecom, have been analyzing for years.

"A trench would need or be constructed for four tracks initially," Kamhi said. "Otherwise it would be extremely difficult to navigate the creek issues and to be able to realign the tracks."

The city has yet to analyze what it would cost to build a four-train trench or the engineering challenges it would entail. Prior analysis, however, suggests that these challenges would be significant.

Even a two-track trench would require the city to divert Barron and Adobe creeks through siphons and lift stations and to pump groundwater along the entire length of the segment. Widening the corridor to four tracks would only add to these challenges.

Councilmember Vicki Veenker suggested at the Nov. 21 meeting that a four-track trench would be "wildly expensive," while Councilmember Ed Lauing wondered whether the new analysis should prompt the city to eliminate some of the alternatives currently on the table.

Burt, meanwhile, advocated for additional analysis to see whether the trench alternative would still be viable with the four-track option.

"The dilemma is, whether we think high-speed rail is coming or not, we and Caltrain have to do grade separation in ways that allow for four tracks in a given location," Burt said.