Elsewhere in the area, several people had to be rescued from cars stranded while motorists tried to drive through flooded roads, including a woman who was rescued by boat.
While Guerneville seemed to have the worst rain and flooding, other towns also faced damaging water and evacuations, as the Russian, Napa, Sacramento and other rivers topped their flood stages.
Meanwhile, the town of Guerneville and neighbouring Monte Rio are described as islands - cut off by flooded roads.
The waterway is forecast to crest at 46 feet around 9 p.m. Wednesday, and the Sonoma County Sheriff's Office said the town of Guerneville is landlocked.
ABC 7's Amy Hollyfield got as far as the Farmhouse Inn on River Road in Forestville, which had to be evacuated Wednesday as flooding reached its driveway.
Local officials described Guerneville and neighboring Monte Rio as "islands".
About 2,600 homes, businesses and other structures in the popular tourist destination were flooded by water up to 8 feet (2.4 meters) deep and at least 3,500 people were ordered to evacuate.
Click through the slideshow above for an aerial perspective of the event.
The National Weather Service forecast the Russian River would remain above flood level until late Thursday night. Wick says they expect that to happen by Friday afternoon.
The unidentified man was trying to walk from a barn to his home in Ferndale through up to 5 feet (1.5 meters) of water Wednesday evening when he was carried away by the fast-moving current, said Samantha Karges, a spokeswoman with the Humboldt County Sheriff's Office.
More rain is expected later this week, though. The record peak for the Russian River is 49.50 feet in 1986, the National Weather Service reported.
As of Thursday morning, waters were finally beginning to come down, and there had been no calls for emergency rescues in Guerneville overnight, the sheriff's office said.
Some places were standing in 8 feet (2.44m) of water and residents were using kayaks and boats instead of cars.
Residents awoke Thursday to sunshine and began assessing the damage while the water started receding.
The governor's office said the emergency proclamation was issued for the counties of Amador, Glenn, Lake, Mendocino and Sonoma to help communities respond to and recover from unsafe flooding, mudslides and damage to critical infrastructure.
Here's what the Sonoma County flooding looks like on the ground.
Rhondell Rasmus had pulled to the side of a road too flooded to cross in Sebastopol in Sonoma County late Tuesday night and emergency dispatchers told her to wait for help. On some streets, the water reached the windows of cars.
He says two were on a boat without paddles and one had to be rescued from a tree after driving her vehicle into floodwaters.
The evacuation orders affected about two dozen communities stretching dozens of miles along the river.