The overwhelming majority of write-ins are expected to be for Frye, 52, who is ''extremely optimistic" she will win once all the ballots are counted.
Frye, a Democrat, campaigned on change in this historically Republican seaside city of 1.3 million people, the nation's seventh-largest.
Murphy was beset by a deepening scandal that has prompted federal investigations into whether officials hid bad news about an underfunded retirement plan from investors and taxpayers.
Murphy was forced repeatedly to deny rumors that the city faced bankruptcy. Five days before the vote, talks between the city and its new auditor appeared to break down.
Adding to that, three of nine City Council members were indicted last year on federal charges of taking bribes from a strip-club owner who had sought to ease restrictions on touching dancers.
Two pleaded not guilty and remain in office, while the third pleaded not guilty. Charges were dropped after he died in August of liver illness.
''Everybody's sort of feeling bad about being in San Diego," Frye said at a campaign stop last week. ''Right now, what we need to do in this city is lighten up a little. In fact, we need to lighten up a whole lot."
Frye was a striking contrast to her opponents.
She has weathered skin, speaks in surfer lingo, and wears colorful suits; Murphy and fellow candidate Ron Roberts, a San Diego County supervisor, lean toward dark suits and have worked in government for years. Frye, the wife of legendary surfer Skip Frye, was elected to the City Council three years ago.
She differed with her opponents on hot-button social questions. Murphy and Roberts backed keeping a Boy Scout camp in a city park; Frye supported those who say the group discriminates against gays and atheists.
Murphy and Roberts opposed plans to distribute clean needles to potential drug users; Frye argued doing so would reduce the spread of AIDS and other diseases.
''Basically the Republicans split the vote and the Democrats all rallied around one person," said Sam Hardage, a former chairman of the San Diego County Republican Party.
Frye often is on the losing end of lopsided City Council votes. In 2002 she was the lone dissenter in a vote to enhance retirement benefits -- one that Murphy said he regretted.
She also has boycotted some closed-door meetings to protest what she considers a culture of secrecy at City Hall.
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