Former Fairfax City treasurer Frances L. Cox deposited more than $100,000 in cash in personal bank accounts scattered across Fairfax County during her last year as city treasurer, witnesses said yesterday in the third day of her embezzlement trial.

The cash deposits, mostly in small bills, totaled as much as $14,000 per month, witnesses said, as the prosecution concluded its case against Cox in Fairfax Circuit Court. Prosecutors have alleged that Cox stole the money from the city in a protracted, but unsophisticated embezzlement scheme.

"She would have a stack of bills, mostly 20s, 10s, 5s," Debra Hollister, a teller at the former National Bank of Fairfax, testified. She said Cox appeared at the bank one or two times a week to make cash deposits. "Occasionally there would be a $50 or $100 bill . . . but it was mostly 20s." She said Cox also deposited her payroll check every two weeks.

Cox, treasurer for 27 years before she was defeated in last fall's elections, has pleaded innocent to the indictment charging her with embezzlement of an unspecified amount of money.

Prosecutors finished two days of testimony yesterday with bank officials and other auditors who said Cox deposited $109,271 in cash into her personal accounts at three Northern Virginia banks in 1981.

Attorney John H. Rust Jr. launched Cox's defense yesterday with testimony from city auditors who said they found money misplaced in the treasurer's office but found no evidence of fraud or criminal wrongdoing.

Cox's monthly cash deposits at the First American Bank dropped from $8,240 in December 1981 to $200 in January 1982 after she left office, Gregory Polland, an auditor who investigated Cox's personal accounts testified. She deposited another $200 in cash in February, after which cash deposits ceased, said Polland.

Deputy Fairfax Commonwealth's Attorney Steve Merril argued that Cox substituted cash received in the treasurer's general fund with checks from real estate and personal tax funds in an attempt to cover the missing money.

Rust argued that any discrepancies in the city treasurer's office were caused by sloppy record keeping. not criminal wrongdoing by Cox.

"We found numerous cases . . . where deposits were misclassified," said Helen Denton, a representative of an accounting firm hired to audit city records from 1972-78. Denton who said the city paid her firm an extra $25,000 in 1978 to attempt to untangle treasury records said she found no evidence of criminal wrongdoing.

Auditor Paul Cumiskey, who worked on city audits from 1979-81, said his firm found errors in city records, but also found no evidence of wrongdoing.

"An audit of a financial statement is not designed to detect fraud," Cumiskey said during a cross-examination by Merril. "We did report to the city on control weaknesses."

As the prosecution ended its case, Rust criticized Judge Barbara Keenan for her handling of the trial and pressed for a mistrial. "Repeatedly you've characterized the evidence giving your interpretation of the facts in dispute to the jury," Rust said when the 12-member jury was out of the courtroom. Keenan denied the request.

Rust also was unsuccessful in his attempt to throw out prosecution evidence concerning Cox's personal bank accounts, claiming Merril never proved money was actually missing from the city treasury when he attempted to link missing funds to Cox's private bank account deposits. Keenan ruled the evidence admissible.