R. Craig McNamara stood slightly apart from the crush of television cameras and cardboard boxes, looking by turns dismayed and amused by the raucous carnival that marked the bidding deadline Wednesday for the government's proposed $6 billion atom smasher.

"This," he said incredulously, "is really something."

McNamara, a walnut farmer from Winters, Calif., is the odd man out in the frenzied competition to land the biggest federal project in decades. California officials brought the Energy Department 800 pounds of documents explaining why the so-called supercollider should be built in their state; McNamara came bearing a four-ounce volume explaining why it should not be built in his county.

Relatively few opponents have surfaced since President Reagan gave the green light last January to the 53-mile-long superconducting supercollider. Most are members of Congress and scientists fearful that the gargantuan project will drain federal coffers of money needed for other scientific research.

"The federal government is great at doing these mega-projects that are big and splashy and involve billions of dollars," said Rep. Don Ritter (R-Pa.), a leading opponent. "But there's a race for our technological life going on, and everybody knows that it's going to squeeze out other science."

McNamara's opposition, however, comes from another direction. Behind the silver lining of federal greenbacks and high-tech prestige, he sees a big cloud hanging over the lush farmland of the Central Valley.

You might call him the tack in the elephant's toe, leader of a low-budget movement seeking to divert a multibillion-dollar project avidly sought by state officials and the politically powerful University of California system.

As the son of former defense secretary Robert S. McNamara, the sandy-haired Californian gets a certain amount of deference from state officials. But he makes it clear that his father, while supportive, is leaving this battle to his son.

The site McNamara is seeking to protect, one of two proposed by California, is in Yolo and Solano counties, near the city of Davis. State and university officials envision the supercollider encircling the University of California-Davis like a halo.

Promoters contend the site is perfect: attractively rural with plenty of open land for the accelerator's underground tunnel and above-ground laboratories yet close to the urban amenities of San Francisco and the university atmosphere that scientists will surely expect.

In his 20-page "statement of disqualification," McNamara points out a few characteristics of the proposed site that California has not touted.The area is criss-crossed with seismic faults, including the Midland Fault, which is suspected of being responsible for the 1983 earthquake that devastated the Central Valley town of Coalinga. State officials acknowledged this week that the site was initially rejected because of earthquake potential, but said they believed it would meet DOE's requirements. Ground-water tables in the area are high, and the site lies within the 100-year flood zone. Excavating the collider's tunnel would require expensive "dewatering" techniques that could dry up nearby irrigation and drinking wells and contaminate ground water, and the tunnel would leak during operation. A preliminary state environmental report conceded the disadvantages, but said they could be "minimized," partly by cleaning up contaminated ground water for irrigation use. The site sits astride one of the most productive agricultural areas in the nation, and building it would violate the spirit and letter of federal, state and county laws aimed at minimizing the loss of prime farmland. The state says about 7,500 acres of farmland would be displaced, but agricultural zoning would be retained "to the maximum feasible extent."

Part of that lost farmland would be McNamara's. About 120 acres of his 520-acre walnut and tomato operation lie in the proposed path of the supercollider. But he contends that the economic boom and high-tech development expected to follow the supercollider could damage the agriculture future of the entire Central Valley -- farmland that the government has spent billions of dollars to bring into production.

"It is difficult to conceive of a more inappropriate location," McNamara said. "It just doesn't make any sense."