As the California agency charged with building high-speed rail finalizes its plans for the Peninsula segment of its contentious system, Palo Alto officials are raising alarms about a feature that is conspicuously missing from the proposed design: grade separation.

City leaders have been raising concerns about the potential impacts of the high-speed rail system ever since late 2008, when voters approved a $9.95 billion bond for the San Francisco-to-Los Angeles line. Local sentiments turned sharply against the project shortly thereafter after the California High-Speed Rail Authority unveiled a four-track design that raised fears about local properties being seized to accommodate the new system and prompted Palo Alto City Council members to take an official stance against the project which they argued is neither financially viable nor particularly desirable.

The initial panic has abated over the past decade, as Palo Alto and neighboring cities successfully lobbied lawmakers and the rail authority to switch the design from a four-track alignment to a "blended system" in which Caltrain and high-speed rail share two tracks on the Peninsula. At the same time, the rail system became stymied by funding shortfalls and political roadblocks in Sacramento as its price tag jumped from an initial estimate of about $33 billion to more than $100 billion under the latest calculations.

Now, however, high-speed rail is back in the spotlight. In June, the state Legislature agreed to release $4.2 billion from the 2008 funding for the construction of the system and to appoint an inspector general to oversee the stalled project. The rail authority also released in June its final Environmental Impact Report for the segment between San Francisco and San Jose. Its board of directors is set to review and approve the document on Aug. 17 and 18.

The release of the environmental analysis comes at a pivotal time for the Palo Alto council, which is now finalizing its plans for grade separation — the realignment of rail crossings so that tracks would not intersect with local streets at three crossings: Churchill Avenue, Meadow Drive and Charleston Road. This week, the council agreed to place on the November a business tax that would help fund grade separation, a project that is expected to cost hundreds of millions of dollars and take more than a decade to complete.

The high-speed rail project could conflict with these plans. The recently released environmental analysis evaluates two alternatives, both of which generally stick to the two-track "blended system" design. The main difference is that one of the alternatives also includes a 6-mile, four-track passing track between San Mateo and Redwood City, an aerial viaduct near the San Jose Diridon Station and a maintenance facility in Brisbane. The analysis concluded that the alternative without the passing tracks is the environmentally superior option, a conclusion that the city generally supports.

Palo Alto officials are concerned, however, that the analysis does not consider an alternative in which rail crossings are grade-separated. Instead, the analysis proposes to install four-quad gates at the rail crossings to prevent cars from entering the tracks when trains are passing. While this option would enhance safety, it would do little to alleviate local concerns about traffic jams that would occur around the rail crossings as Caltrain enhances train service and the high-speed system begins operations on the Peninsula.

A new report from the city's Office of Transportation takes issue with the rail authority's conclusion that traffic impacts relating to traffic circulation and emergency response are significant. The environmental analysis concluded that 41 out of 49 at-grade crossings between San Mateo and Palo Alto would operate at levels of service of "E" or "F" — the two lowest grades — in 2040 if high-speed rail is operating. It also found that 27 of these intersections would be affected by the rail project during the morning and afternoon peak hours.

Some of the worst delays would occur at intersections adjacent to the Meadow Drive and Churchill Avenue in Palo Alto, which would experience increases of 187 seconds and 334 seconds, respectively, during the peak morning hours. Only the Brewster Avenue crossing in Redwood City would see a greater delay, with a projected 387-second increase at the Perry Street and Brewster Avenue intersection during the morning peak.

The environmental analysis also identifies numerous local intersections that are projected to have a low level of service even without the rail project but that would suffer further adverse impacts under either high-speed rail alternative. These include the intersections of El Camino and Sand Hill Road; Alma Street and Palo Alto Avenue; Churchill Avenue's intersections with Alma and Mariposa Avenue; and Park Boulevard's intersections with Meadow Drive and Charleston Road.

Palo Alto staff strongly disagrees with the rail authority's conclusion that the "significant and unavoidable" traffic impacts identified in the report cannot be mitigated, according to the new report. Specifically and significantly, it fails to consider the most obvious — albeit complex — way to curb traffic: separating tracks from roads, the city is arguing.

The subject of grade separation and its potential conflict with high-speed rail came up at recent meetings of the council's Rail Committee, which in June approved new guiding principles that take up the topic. The guiding principles, which the council is set to adopt this Monday, Aug. 8, state that Palo Alto believes that the California High-Speed Rail Authority "must coordinate with Caltrain as the lead agency and should fund the study and construction of any potential passing tracks and, if needed, grade separations or modifications to grade separations and should not commence service until they are complete."

Nadia Naik, who co-chaired a citizen panel that helped the city come up with grade-separation alternatives, proposed the principle at the committee's June 15 meeting.

"There is a weird scenario where we build a grade separation in the future and then high-speed rail comes along and decides they want to change something," Naik said.

In addition to ratifying the new Rail Committee guiding principles, the council is scheduled to approve a letter to the rail authority urging it to study an alternative that includes grade separation. The letter, which is signed by Mayor Pat Burt, asserts that grade separation "would reduce this identified significant and unavoidable impact to a less than significant level and therefore must be analyzed" and claims that the rail authority is unfairly burdening the city with the cost of analyzing the traffic impacts of the rail system.

"The City continues to assert that impacts to all elements combined, including vehicular, bike and pedestrian safety, delays, and emergency response warrants analysis of grade separation as an alternative to the proposed project or as mitigation," the letter states. "Proper analysis of the reasonably foreseeable future condition would only further demonstrate the need for a comprehensive plan to address the identified impacts such as grade separation."

Past entreaties by the city for the rail authority to study grade separation have failed to sway the state agency. When City Manager Ed Shikada asked the rail authority in 2020 to study grade separations, the state agency rebuffed the request with a statement that such options "considerably widen a rail project's footprint." The infrastructure that supports grade separation can extend well beyond the roadway crossing to accommodate the fact that changes in railway slope must be gradual, the rail authority stated.

"In other words, it may not be possible to construct only one grade separation in some areas, where close proximity of at-grade crossings means that constructing one grade separation would then require constructing multiple other grade separations," the rail authority's response states. "This can increase the cost of a grade-separated rail alignment. It can also increase the costs associated with right-of-way acquisitions, require additional infrastructure, and increase construction disruption."