Ayotte, the first-term Republican who's trailing Democratic challenger Maggie Hassan in the polls, all but admitted that Clinton is poised to win the White House on Monday.
"There's so much at stake in this presidential election: the Supreme Court, our national security, so many issues that matter to people of this state," Ayotte told CNN's Manu Raju in an interview.
"And Gov. Hassan is going to essentially follow Hillary Clinton's lead on all of them, where I'm going to stand up to her when she's not taking us in the right direction," Ayotte said.
Her comments come as Democrats -- who hope to win control of the Senate and narrow the GOP's House majority on November 8 -- try to make sure it's not easy for Republicans like Ayotte to back away from a nominee they'd supported for months.
Hassan says she's counted 35 times her Republican foe has expressed support for Trump.
Most prominently: Ayotte said in a televised debate with Hassan that she would call Trump a "role model" -- a statement she retreated from just hours later.
On Monday she sought to explain that moment, saying: "I corrected that because I made a mistake. I mean debates many people are -- you're asked a lot of questions at a debate. But it's clear to me that neither Donald Trump nor Hillary Clinton, unfortunately, are role models."
She pointed to Trump' bragging about sexually assaulting women on a leaked 2005 "Access Hollywood" tape as the breaking point between her and her party's presidential nominee.
"I've looked at this whole thing in terms of doing what I thought was in my heart given what happened on those tapes and having a daughter (rather) than any election. But I know that the people of this state understand. And I'm going to fight for them," she said.
Still, Democrats are eager to hang Trump around Ayotte's neck even though she's distanced herself from him -- arguing that the move was purely political.
"Her political calculation in deciding to disavow him truly at the eleventh hour I think just really reflects that all of her judgments are political calculations," said Ayotte's Democratic challenger, Hassan.
She pointed to Trump's attacks on the Gold Star Khan family and other controversies the GOP nominee had stirred up, as well as a host of prominent military figures saying Trump is unfit to be commander-in-chief.
"She could have disavowed him then, but she stuck with him 'cause she thought she needed to politically," Hassan said. "And for her to now suddenly disavow him means either she thought everything he did before that was all right -- which shows extraordinarily bad judgment -- or she was sticking with him because everything for her is a political calculation."
Ayotte, meanwhile, pointed out she's been critical of Trump on a number of occasions -- even if she didn't reject the GOP nominee outright during those controversies.
"I stood up and called Donald Trump out on many occasions -- and that tape, for me, having been a prosecutor, was fundamentally different," she said. "And that, for me, is why I'm not voting for him -- but I'm not for Hillary Clinton either."
Ayotte said she plans to write in the Republican vice presidential nominee, Indiana Gov. Mike Pence, for president.
Polls in New Hampshire have shown Hassan and Ayotte neck-and-neck -- and Hillary Clinton, in a visit to the state Monday alongside Massachusetts Sen. Elizabeth Warren, is expected to link Ayotte to Trump.
Ayotte, though, sought to cast herself as an independent alternative to Hassan's support for Clinton.
"If you look at what's happening, you've got Hillary Clinton's super PAC, Mike Bloomberg's super PAC, you've got Harry Reid's super PAC all throwing millions of dollars in this race to prop up Gov. Hassan," she said. "I think we know you know who she's going to follow in representing the people of New Hampshire."