O'Brien benched Tom Savage at halftime of Houston's 29-7 loss to the Jaguars on Sunday. Savage lost two fumbles — one that was returned for a touchdown — and threw for just 62 yards as the Jaguars built a 19-0 lead by halftime.
Watson, who guided Clemson to the national championship last season, led the Texans to their only touchdown on his first drive, but lost a fumble and threw an interception after that as Houston failed to score again.
"We've got a quick turnaround here so we've got a lot of film to watch, a lot of things to get caught up on," O'Brien said.
"We just weren't in synch," Savage said about his performance on a day when Houston allowed a franchise-re cord 10 sacks. "That's kind of what it was. Holding onto the ball a little too long, trying to make some plays downfield and the game is not meant to be second-and-15."
The crowd, who had booed Savage for much of the first half, cheered loudly when Watson trotted onto the field for the second half. He didn't waste any time getting going, throwing a 4-yard touchdown pass to DeAndre Hopkins on his first drive to cut the lead to 19-7 early in the third quarter.
"The decision to go with Deshaun had more to do with could we find a spark, could we find somebody that maybe could make a play, that could escape the pocket," O'Brien said. "I thought that Tom hung in there and played very tough. But we had a hard time protecting him so I made the decision to go with Deshaun."
Houston's quarterback woes are the latest in years of problems at the position. Watson is the ninth quarterback to play for Houston in the past five years as the team has struggled to find a consistent signal caller.
They signed Brock Osweiler to a $72 million contract before last season, but he was benched late in the season and traded to Cleveland in March.
Savage spent all of camp as Houston's starter despite the team trading up 13 spots to draft Watson with the 12th overall pick.
Watson was 12 of 23 for 102 yards and had two carries for 16 yards on Sunday.
O'Brien was asked to evaluate the play of both quarterbacks.
"Tom plays very calmly," O'Brien said. "I think he knows how to operate our offense. I didn't see him have, when it came to X's and O's, any mental mistakes. There are things that he can do better, things that I can do better to help him."
Then he moved on to Watson.
"Deshaun went in there and made some plays," he said. "Deshaun's a playmaker. He can make plays with his feet. He knows what to do. He checked us in and out of plays. He has good instincts out on the field."
O'Brien was asked if he wished he would have given Watson more snaps with the first team in camp and this week in practice so he could have built a better rapport with Hopkins.
O'Brien said that Watson got plenty of work with the first team and that it wouldn't have mattered if he got more work since Hopkins was out with a thumb injury for most of camp.
Hopkins finished with seven receptions for 55 yards, with six of his receptions coming on passes from Watson. He said he and Watson need to work on some things this week, but he was impressed with his work overall.
"That's what he needed, to go out there and get his feet wet," Hopkins said. "Even though the circumstances where what they were I think he came in and went with the flow."
"It was all right," Watson said of his performance. "A learning lesson. You live and learn. First career NFL game so there's a lot to learn from."
Whether Watson or Savage starts on Thursday, the Texans will have to find a way to protect the quarterback better.
The line was terrible on Sunday without veteran left tackle Duane Brown, who is holding out. It was also the first career game for center Nick Martin, who missed all of his rookie season in 2016 with an injury.
"There's a lot of different things that we can do from a scheme point," O'Brien said. "There's a lot of different things that the players need to do from a playing standpoint. Everybody in that room in there needs to improve."
O'Brien said he'll evaluate many things in deciding who to start against the Bengals, but that one thing carries more weight than the others.
"I look at what happened leading up to game day, how they practiced during the week, but mostly how they play in the game when the lights are on," he said.