Merrick and 2006 tournament winner Maggert registered four-under-par 66s on a day that grew increasingly windy and featured a crowded leaderboard with 15 players within two strokes of the leaders.
Alone atop the leaderboard at five-under, late finisher Merrick hit his tee shot at the last hole into the water on his way to a bogey.
Tied for third at 67 were Americans Jeff Overton and J.J. Henry, along with India's Arjun Atwal and Noh Seung-yul of South Korea.
US Open champion Rory McIlroy of Northern Ireland, trying to make the cut for the first time in four tournaments, was among 11 players bunched at 68.
Others posting two-under-par rounds included US Davis Cup captain Davis Love III and his fellow former Major winners Lee Janzen, Padraig Harrington and Yang Yong-eun.
John Daly, a former resident at the Southwind course and another former Major winner, also posted a 68 but stood out from the crowd with a bright orange shirt and wildly patterned brown pants.
McIlroy, just back from having a practice turn at Olympic in San Francisco where he will be defending his US Open crown next week, was pleased with his round.
"I felt like that was about the best round of golf I played in a while," the Briton said. "It could have been a lot better.
McIlroy stumbled when he was on three-under at the third hole, his 12th, when his approach shot found the water fronting the green and he went on to two-putt from seven feet for bogey.
Otherwise, he was satisfied.
"Off to a decent start, definitely. Lot of good signs out there," he added. "I'm getting the club in a better position. From there you have a little bit of freedom.
"You're not trying to protect against a bad shot. You're trying to hit the shot you can see."
Maggert said he took advantage of his early tee time when he encountered calm conditions.
"I knew the golf course was going to be a little bit easier the first couple hours this morning being first off, so I was able to take advantage of that and just played really solid on my first nine holes," he said.
Regaining his form after undergoing shoulder surgery, Maggert ran off four birdies in five holes from the 12th, his third hole of the day.
After the turn, Maggert eagled the par-five third hole by reaching it in two and sinking a seven-foot putt.
"I had shoulder surgery last year and missed about four, five months," the 48-year-old American said. "But the surgery was fantastic and I feel like I'm a hundred per cent now."