The crash occurred around 10:30 a.m. Saturday at a convergence in the Wilmington River, about seven miles east of downtown Savannah in Chatham County.
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Nine people were aboard two boats -- six in one, three in the other, officials said. The boats were traveling in opposite directions when witnesses said they collided, according to the Georgia Department of Natural Resources.
Initially, two people were confirmed dead and three injured following the crash, the department said.
The Georgia Department of Natural Resources identified the victims Sunday as Christopher David Leffler, 51, of Savannah; Lori Lynn Leffler, 50, of Savannah; Zachary James Leffler, 23, of Alpharetta; Nathan Leffler, 17, of Savannah, and Robert Steven Chauncey, 37, of Savannah.
Chris Leffler was a coach and teacher at Calvary Day School, and Nathan Leffler was a senior at the school, Dr. Hunter Chadwick, head of the school, said in a statement.
"We are saddened to report the death of our faculty member, Mr. Chris Leffler, and his wife, Lori, their sons, Zach and Nate, who passed away from injuries sustained in a boating accident this weekend," the statement read.
The family was "loved by so many and will be missed dearly," Chadwick said, describing Chris Leffler as an "outstanding" teacher, coach and friend.
Nate Leffler "had a quiet demeanor, contagious smile and passion for athletics," Chadwick said. "He was well-liked by his peers, was a great brother and a loving son."
Three men were missing in the wake of the incident -- a 37-year-old man and two men in their early 20s -- but were found Sunday morning, according to the U.S. Coast Guard.
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Mark McKinnon, communications director for the Georgia Department of Natural Resources, told ABC News that all three bodies were found Sunday morning after game wardens detected them with sonar technology around 9 a.m. ET.
The bodies were found close to one another in 14-foot-deep water near the site of the crash, McKinnon said.
Savannah ABC affiliate WJCL captured a damaged boat being towed on Saturday.
"Rough day today out here," Bill Koster, the chief of operations for Chatham County Emergency Services, told reporters.
First responders, including Georgia Department of Natural Resources game wardens, Chatham County Marine Patrol, Savannah Fire and Chatham Emergency Services and two U.S. Coast Guard helicopters, helped look for the missing boaters.
Four passengers sustained minor injuries and were transported to a local hospital, officials said. One patient was flown to the hospital by the Coast Guard after being rescued from the water, Koster said.
Mark Christopher Stegall, 45, has been charged with boating under the influence, McKinnon told WSAV-TV.
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No lawyer who could speak on Stegall's behalf is listed in Chatham County Jail booking records.
The names of others involved were not immediately made public.
Two center console boats were involved in the incident, one of which sunk following the crash, Koster said.
Chatham Emergency Services urged people to avoid the area following the deadly accident.
The crash is the second involving a boat and serious injuries on the Wilmington River this month. A local businessman was killed May 5 when a boat he was aboard struck an unlit channel marker near the Savannah Yacht Club and he was hit on the head by an unknown object, authorities said.
Saturday was the start of the long Memorial Day weekend, one of the busiest of the year for recreational boaters.
The Associated Press & ABC News' Meredith Deliso, Victoria Arancio, Lillian Gifford, Jason Volack and Will McDuffie contributed to this report.