The incident occurred at a mobile home in the 4500 block of Lakewood Road.
Deputies were summoned by a 911 call just before 4 a.m. to reports of a suicidal man with a gun, Everett police spokesman Aaron Snell said.
"Ultimately it is believed that a domestic dispute spurred this call," Snell said.
There was a standoff with deputies, and about 5:30 a.m., one of the officers shot the man, 36, in the hand, Snell said.
The man's injuries were not believed to be life threatening. He was taken to an Everett hospital and then moved to Harborview Medical Center in Seattle for more treatment, Snell said.
The man reportedly had immediate access to weapons. Whether he was carrying a weapon at the time he was shot was among the details being reviewed by the Snohomish Multiple Agency Response Team, Snell said.
As is standard in such cases involving use of force, the circumstances were being investigated by the special countywide team of detectives.
The deputy, who has been with the department for seven years, was placed on paid administrative leave, which also is standard practice in officer-involved shootings.
The incident took place across the road from Lake Goodwin in a neighborhood with several other mobile homes. Passersby slowed as they passed the yellow crime scene tape that was tied between a telephone pole and mailboxes leading into a gravel driveway.
Behind the tape, detectives were knocking on doors and talking to potential witnesses Thursday morning.
This was the second line-of-duty shooting for sheriff's deputies this summer.
Matthew Wiese, 46, was fatally shot in June outside his parents' Lynnwood-area home after allegedly pointing a gun at deputies. Before the shooting, Wiese had lobbed fireworks at police.
The deadly confrontation happened after deputies were called to investigate allegations that Wiese violated a protection order obtained by his wife.
The slain man's father later told an Everett police sergeant that his son took some medications for mental illness, court records said. Wiese's death remains under investigation.
Snohomish County Executive John Lovick recently announced plans to convene a panel to find ways to improve services for people living with mental illness. The panel is expected to begin meeting in September. The executive is recruiting mental health professionals to look at crisis services, access to care, and gaps in services.
Diana Hefley contributed to this story.
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