Caltrain's plan to power its trains by electricity rather than diesel is expected to improve service, help the environment and boost ridership and revenues for the agency when its first modern trains roll out in 2019.

But for Palo Alto, which boasts the second busiest train station in the entire system, these improvements come with a bitter pill: a significant and unavoidable worsening of traffic conditions at three already congested intersections of Alma Street.

Even as Caltrain touts its electrification plan as an important way to get cars off the roads, it acknowledges in its environmental analysis that several streets near the 51-mile corridor will see traffic conditions go from bad to worse. Alma is atop this list.

According to the in-depth Final Environmental Impact Report that the Peninsula Corridor Joint Powers Board, which operates Caltrain, is expected to certify Thursday morning, the problems at the Alma intersections cannot be eased through strategies such as lane reconfigurations and new traffic signals. Because the train corridor is bounded by Alma to the east side and homes and businesses to the west, it cannot be widened. Thus, traffic problems at its intersections with Charleston Road, Meadow Drive, and Churchill Avenue will remain "significant and unavoidable," according to the EIR. The report states that "no feasible mitigations exist" to change this; thus, none are proposed.

Palo Alto's three intersections are among 17 systemwide that could not be improved, leaving each with a "significant" level of delay. (There are 89 intersections along the entire corridor, from Gilroy to San Francisco.)

Another Palo Alto intersection, at Palo Alto Avenue near Sand Hill Road, would also have traffic problems, though Caltrain expects to reduce the delays by widening Sand Hill and adding a traffic lane that would allow southbound cars to turn on red.

Palo Alto, which has in the past supported the $1.5-billion electrification project, raised concerns about the plan in a letter to Caltrain last April. The letter, signed by then-Mayor Nancy Shepherd, requested that the environmental document explore a dramatic option that would fix the predicted traffic problems: grade separation of the tracks and the streets (effectively creating underpasses or overpasses).

In the letter, the city requested that Caltrain establish a fund with which to explore various ideas, most notably placing the Caltrain corridor in a trench. Palo Alto also requested that Caltrain's environmental analysis consider whether the electric equipment and new substations will harm the city's future ability to construct grade separations.

"Grade separations are an important issue in the Peninsula, and not something that can be ignored in this EIR given local traffic and safety concerns," the city wrote in April.

Yet its request has gone largely unanswered. The EIR notes that while grade separations are a "technically feasible mitigation," it is "financially infeasible for Caltrain to adopt a comprehensive program of grade separations as mitigation."

"However, in the long-term where funding becomes available and it is acceptable to local jurisdictions, Caltrain would support grade separations in the long run," the Final EIR states.

In detailing the difficulty of trenching the rail line, the environmental report stated that Caltrain would have to relocate the overhead contact system (OCS) that will connect trains to the electricity infrastructure.

The document says nothing about the cost or the design, engineering and construction challenges of moving the equipment once it's installed to accommodate a trenched system.

Alternately, there would "usually be little to no need to relocate any portion of the OCS" if the roadways were submerged under the Caltrain tracks, Caltrain officials wrote.

Local support for building a trench along the Caltrain corridor has been growing since 2009, when Palo Alto officials and residents began their campaign to stop the California High-Speed Rail Authority from constructing an elevated four-track system along the tracks. The hugely unpopular proposal was ultimately scrapped and the rail authority agreed to pursue a "blended system" with Caltrain, one in which the two train services would share the same set of tracks along the Peninsula. In early 2013, the city adopted the Palo Alto Rail Corridor Study, a planning document that advocates for a below-grade track system and improved east-west connections across Alma Street, the Caltrain tracks and El Camino Real.

Caltrain's EIR briefly acknowledges the document and its recommendation to trench the train, though it points out that the study is "dominated by concerns about the high-speed rail project." But this statement is not entirely accurate. The Palo Alto study makes it clear in its introduction that it represents the city's response "to planned rail investments along the Caltrain rail corridor, specifically the California High Speed Rail project and potential modifications to Caltrain operations."

According to Caltrain's EIR, the three Alma intersections are expected to operate at "Level F" (the worst possible congestion) whether or not the project proceeds, though things would get worse if it does. At the intersection of Alma and Charleston, cars could wait 2 minutes or longer in 2020, regardless of electrification. Having the project in place would add 28 seconds to the wait during the morning peak hour and 9 seconds during the evening peak. On Alma and Churchill, the wait would go from 83.9 seconds (already an "F" level) during the morning peak if the project is not implemented to 108.9 seconds if it is. A similar increase would take place during the evening peak on Alma and Meadow Drive.

In its April letter to Caltrain, Palo Alto had also requested that Caltrain improve bicycle and pedestrian amenities as part of the modernization project, either at the intersections or the Caltrain stations.

"Given the increased traffic identified in the DEIR (Draft Environmental Impact Report), pedestrian and bicycle safety improvements must be addressed in the FEIR (Final Environmental Impact Report); however, any pedestrian and bicycle improvements must emphasize safety," Palo Alto's letter, signed by Shepherd, states.

In response, Caltrain pointed out in the final EIR that there is "no evidence that additional bicycle and pedestrian facilities would meaningfully change the amount of bicyclists or pedestrians using Caltrain or have any meaningful effect on reducing traffic at the affected intersections." The report thus did not propose any bicycle or pedestrian improvements.

Caltrain's decision to include no mitigations at all for the most impacted local intersections did not please Palo Alto officials, who fired off another letter on Dec. 31.

"The FEIR clearly states for the Churchill, Meadow and Charleston grade crossings ... that 'no feasible mitigation was identified.' This response is not acceptable to the City, and at a minimum, the City requests that the Joint Powers Board set aside funds for design and engineering of grade separation solutions along the corridor," the letter states.

Caltrain's analysis makes another argument that Palo Alto officials find troubling: that the long-planned electrification project isn't subject to the California's environmental laws. This argument did not appear in the draft EIR but has been inserted into the final document.

In the Final EIR, Caltrain officials claim that they don't even have a legal obligation to put the document together but are "voluntarily adhering to the strictures of CEQA (California Environmental Quality Act)," a law that aims to protect communities from the impacts of new developments and major projects and initiatives. In an apparent reference to a recent ruling regarding high-speed rail, the Caltrain EIR claims that a number of "court and regulatory decisions have held that the construction improvements and operation of federally regulated railroads are exempt from state environmental regulatory laws, including CEQA."

The Final EIR states the Caltrain board "expressly preserves its ability to assert preemption if legal challenges to the EIR are initiated."

This argument, and the fact that it was made just before the document's expected certification, was challenged by city officials, who have been assured all along that environmental law will protect their interests.

"Whether legal or not, this assertion being made at the 11th hour is wrong, creates distrust, calls into question the tremendous amount of time and money our City has invested in what we were led to believe was a true CEQA process, and is reminiscent of action taken by the California High Speed Rail Authority that created so much of the distrust regarding rail on the Peninsula we still deal with today," Shepherd's Dec. 31 letter stated. "In addition, it contradicts the many assurances we repeatedly received from Caltrain throughout this process that CEQA would be honored."

Palo Alto Councilman Pat Burt, who had served on the council's now-defunct Rail Committee, said he does not believe that Caltrain had adequately responded to the city's concerns. Though he acknowledged the need to improve Caltrain service to accommodate increasing ridership, Burt told the Weekly he believes the agency should also consider other alternatives in conjunction with the electrification, including longer trains. He also raised concerns about Caltrain's apparent about-face on the issue of CEQA.

"We and the cities along the corridor have been promised for years that CEQA would be the backstop that protected us against significant impacts to improvements to the rail corridor that we otherwise support," Burt said. "And now, they are saying that the most significant impacts in our community are unavoidable and won't be mitigated."

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