From suspicion over the Clintons’ Whitewater dealings to 2008 claims of having braved “sniper fire” in Bosnia to now, where she faces questions over her use of a secret email server to conduct business in the State Department, Hillary Clinton has earned a level of distrust that’s almost unprecedented for a major political party presidential nominee.

New polling shows voters rate Donald Trump as more honest than Mrs. Clinton, underscoring deep questions that have been swirling for decades around the former secretary of state and current front-runner for the Democratic presidential nomination.

Sen. Bernard Sanders, her competitor for the nomination, warns of electoral “disaster” if she’s Democrats’ pick this fall, and analysts say there’s little she can do to truly change the narrative, especially when presumptive GOP nominee Mr. Trump begins his own blistering assault over the summer.

“It’s largely set in stone,” said Cal Jillson, a professor at Southern Methodist University who specializes in presidential politics. “If you think back to Gennifer Flowers, Travelgate, Monica [Lewinsky] and all that stuff, the billing records from the Rose Law Firm, all of that, people know all of this, and it either convinces you that both Clintons are morally flawed — and to have them back in the White House would be disastrous — or you think that, despite these proclivities for scandal, the Clinton years were good years economically.”

“So if you’re going to have a backdrop of scandal but a well-administered national government, or at least a government that works then you can go ahead and vote for Hillary Clinton,” he added.

While voters in the Democratic primary have indeed been voting for Mrs. Clinton, there’s renewed pessimism within the party about her prospects in the fall. New Quinnipiac polling this week shows Mrs. Clinton virtually tied with Mr. Trump in the key battleground states of Pennsylvania and Florida and 4 percentage points behind in Ohio.

At the same time, surveys show Mr. Sanders handily beating Mr. Trump, leading the Vermont senator to suggest the party is doomed with Mrs. Clinton at the top of the ticket.

“For months Bernie Sanders has out-polled Hillary Clinton against Donald Trump, and often by extraordinarily large margins. Because we must do everything we can to defeat Trump in November, our mission is to win as many pledged delegates as we can between now and June 14,” when the primary season ends, Sanders campaign manager Jeff Weaver told supporters in an email Wednesday. “Then we’re going to have a contested convention where the Democratic Party must decide if they want the candidate with the momentum who is best positioned to beat Trump, or if they are willing to roll the dice and court disaster simply to protect the status quo for the political and financial establishment of this country.”

But the Quinnipiac poll highlights nagging issues even more troubling than Mrs. Clinton’s poor performance against Mr. Trump. Voters in Florida, Ohio and Pennsylvania see Mr. Trump as much more trustworthy, and it’s not even close.

In Florida 29 percent of voters say Mrs. Clinton is honest, compared to 38 percent for Mr. Trump. In Ohio it’s 27 percent to 35 percent, and in Pennsylvania just 30 percent of voters say they consider Mrs. Clinton an honest candidate. Thirty-nine percent of Keystone State voters said Mr. Trump is honest.

The problems extend beyond those battleground states. A Gallup Poll released in February found that, for 21 percent of U.S. adults, the terms “dishonest” and “liar” were the first things that came to mind when asked about Mrs. Clinton.

The honesty problem coincides with a massive free fall in Mrs. Clinton’s favorability ratings. In April 2013 64 percent of Americans viewed the former first lady favorably. In April 2015 that number was 48 percent.

Last month it dropped to an abysmal 41 percent, according to Gallup.

Mrs. Clinton’s use of a private email server while secretary of state — which is now the subject of an FBI investigation — has been a leading factor in that decline. Mr. Sanders may have contributed too by relentlessly hammering Mrs. Clinton’s ties to Wall Street, her secret paid speeches to Goldman Sachs and other issues that help paint her as part of the political establishment.

Specialists say the questions about Mrs. Clinton’s trustworthiness go back decades.

“I think it goes back to her period of being very territorial about her position in the White House and her office in the West Wing. She was in a stage of demonizing people, and her enemies became much more suspicious of her,” said William Chafe, a historian at Duke University and author of the book “Bill and Hillary: Politics of the Personal.”

“When she’s in a situation like she’s in now, of being in charge, being the candidate, it’s easier for people to generate suspicions about her,” he continued. “And that makes her more vulnerable.”

Indeed, Mrs. Clinton’s low trustworthy numbers — and sagging favorability ratings — seem to correlate with her being a candidate versus serving in office.

In November 2006, when she was serving as a U.S. senator from New York, just 6 percent of voters said “dishonest” was the top term they associated with Mrs. Clinton, according to Gallup polling.

In April 2008, in the heat of her race against then-Sen. Barack Obama, that number shot up to 15 percent.

The same has been true for her favorability numbers, Gallup data show. In May 2012, after serving nearly four years as secretary of state, her favorability rating was 66 percent.

In May 2015, when the Democratic primary was just beginning, it had already dropped to 50 percent, and now has fallen to an almost-record low of 41 percent.

Analysts say the takeaway is clear: Mrs. Clinton the candidate is an easier target.

“When she’s doing work, she’s perceived as extraordinarily competent. When she’s running for office, she’s seen in a different way,” said longtime Democratic political consultant Hank Sheinkopf. “That’s the nature of politics, because opponents and reporters tend to raise previous controversies, and therefore they become public again.”

The Clinton campaign did not respond to a request for comment.

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