EVERETT — Snohomish County Deputy Executive Mark Soine resigned Monday, leaving a long trail of questions about his management of key government functions during his five years on the job.

Soine announced he was stepping down on the same day the county was served with a nearly $1 million lawsuit claiming mismanagement by him contributed to sexual harassment, discrimination and a hostile work environment against female staff in the county’s planning department.

Soine’s resignation is effective June 3. In a letter sent to Executive Aaron Reardon he told his boss, “the time has come for me to move on” and he needed to devote time to his family.

Lately, the county’s second in command had been absorbing the brunt of complaints about the executive’s office under Reardon. In February, Soine publicly took the blame for the county’s failings in handling harassment cases after an independent review found shoddy record-keeping at the county’s equal employment opportunity office. The attorney in charge of that office, Mark Knudsen, resigned just ahead of the report’s release.

Last week, an audit of the Department of Information Services, which Soine supervised until early this year, found an unusual lack of communication between the department’s managers and their customers in county government. Reardon’s employees reported good service at the same time other county leaders had become so frustrated they’d begun exploring ways of removing control of the computer networks from executive’s office, the audit found.

Soine wasn’t specifically named in the audit, but the report made clear problems with the computer system had more to do with managing people than caring for equipment.

Soine’s role in county government has been the focus of increasing scrutiny since the county’s former planning director, Craig Ladiser, resigned and was later charged with a sexually motivated assault involving a woman who worked as a building industry lobbyist.

The harassment lawsuit filed Friday in King County alleges Soine failed to crack down on sexually charged misbehavior in Ladiser’s planning department, long before the reported attack at a Redmond golf course. It calls the county’s sexual harassment investigations a “black hole.”

In the lawsuit, Debbie McPherson, a former human resources manager in the planning department, claims she was prevented from doing her job and laid off in retaliation for confronting sexual harassment, age discrimination and other inappropriate behavior.

The complaint refers to Ladiser and the other men who ran the planning department as “the Harley Club” and describes a culture of “excessive drinking and motorcycle riding with male managers.” It says that managers gave preferential treatment to other men, mocked disabled employees and ranked the looks of female employees.

The lawsuit alleges that even planning department customers could become the subject of sexual harassment, including a woman who was grabbed while using a copy machine.

When confronted after that incident, the county manager who grabbed the woman allegedly said “I thought it was an employee,” court papers said.

“Soine knew or should have known of the misconduct,” and failed to take appropriate action, McPherson’s lawsuit says.

Soine, 59, earns $161,429 annually. Neither he nor Reardon returned numerous calls for comment Monday. Instead, Reardon sent out a prepared statement saying his office was focused on other challenges and opportunities.

Soine was an Everett city attorney before Reardon hired him in 2005. Until recently, he has most often attracted attention as a tight-lipped standard bearer for Reardon.

In 2007, his refusal to discuss Reardon’s plans for celebrating The Boeing Co.’s rollout of the 787 Dreamliner triggered a spat with the county council that prompted them to temporarily limit Reardon’s ability to authorize spending.

That same year, a state examiner ruled that Soine, acting as the county executive’s chief labor negotiator, had illegally delayed efforts to settle a contract with Superior Court clerks and retaliated against them for forming their own guild.

On Monday, few county leaders spoke as candidly about Soine as they have in the past.

Councilman Mike Cooper said the resignation came as no surprise, given the recent controversies.

“Mark and I had our share of run-ins, just like the rest of the council,” Cooper said. “He was tough and he was there to represent the executive, and he played that role well.”

Cooper also said that though the two often disagreed, Soine always returned his phone calls or agreed to meet in person.

Treasurer Kirke Sievers said he saw Soine’s departure as “collateral damage” for lapses in the executive branch and said that he was sorry to see him go. Sievers also blamed communication problems on employees being afraid to report problems up the chain of command, rather than any shortcomings specific to Soine.

Last week, word was already out about Soine’s impending resignation.

Reardon and his spokesman, Christopher Schwarzen, ignored repeated inquires by The Herald on Friday to clarify Soine’s employment status. The same day, Reardon’s executive assistant, Nancy Peinecke, laughed at a reporter’s question and said Soine was merely on vacation.

This isn’t the first time Reardon’s office has obscured the circumstances regarding a top manager’s continued employment. In July, Schwarzen forwarded an e-mail suggesting Ladiser was out of the office dealing with a “family emergency.”

In reality, the planning director had already been placed on administrative leave and was the subject of a county investigation into his alleged misconduct on the golf course. He’d also entered treatment for alcohol abuse.

Herald writer Andy Rathbun contributed to this report. Noah Haglund: 425-339-3465, nhaglund@heraldnet.com.