Watson will be worked on by team physio Alex Kountouris overnight on Wednesday to try and get him right to bowl again in the second innings.
The opener was free enough to continue fielding and to come out and bat.
However, his long history of breaking down means any niggle must be treated with concern.
Watson (0-7) appeared to pull up short during the last of his four overs and didn't return to the attack.
"There's a little bit of a niggle but he's just going to see Alex and I'm presuming he's going to bowl in the second innings," said coach, Darren Lehmann.
"It's a lower leg. See how he goes."
Australia will be desperately hoping Watson can contribute with the ball in the second innings, however the bigger concern is whether he can back up for the second Test at Lord's next week.
Australian No.3 Ed Cowan also had a tough day at the office, forced off the field at regular intervals during England's innings as he battled a stomach bug.
However, not even a sick tummy could excuse the shockingly loose shot Cowan played to fall to Steve Finn for a first ball duck.
Cowan lashed at a wide one and edged to the slips, with his Test future now looking even cloudier.
The 31-year-old hasn't kicked on to make a hundred since his maiden Test century last year in Brisbane.
The writing was on the wall for him when he was dumped as an opener, however his defensive qualities gave him a reprieve for the first Test at No.3.
But after going away from the reason he was picked and playing a rash shot, Cowan's position is under serious danger unless he can produce in the second innings.
Usman Khawaja is waiting in the wings to assume his No.3 spot for the second Test at Lord's.
England are remaining tight-lipped on Stuart Broad's shoulder injury, after the big quick was unable to bowl on day one after copping a nasty blow while batting.
Broad damaged his shoulder during the Champions Trophy tournament last month, and only narrowly proved his fitness for Trent Bridge.
Australian firebrand James Pattinson hit him with a fierce bouncer, and Broad didn't return as he sought treatment to get it right.
Fellow fast bowler Steve Finn said he, James Anderson and Graeme Swann were prepared to dig in if Broad doesn't return.