A 65-mile section of California’s bullet train through the San Joaquin Valley that a contractor assured could be constructed much more cheaply — with radical design changes — has become another troubling and costly chapter in the high-speed rail project, a Times investigation found.

The segment runs across rivers, migratory paths for endangered species and an ancient lake bed through the length of Kings County. Before awarding a contract for the section, the California High-Speed Rail Authority and its consultants knew about these sensitive issues and prepared lengthy environmental reports aimed at accelerating construction by avoiding legal obstacles.

But in 2014, when the rail authority awarded the contract, it went with the lowest bidder — a Spanish company named Dragados — which promised $300 million in cost savings by altering the design that the authority had proposed to regulators.

Seven years later, these changes have been largely abandoned and have contributed to more than $800 million in cost overruns on the Kings County segment. That figure is 62% above the contract price tag, which the rail authority has agreed to pay, according to interviews and technical and contractual documents reviewed by The Times.

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