Watling, who has played 52 tests and averages 38.05 with the bat, is recovering from a niggling hip injury.
It has prevented him wicketkeeping in ND's past five games so he would be rusty if he had been chosen for the second test, but the injury doesn't seem to be affecting his batting.
He made 115 in the weekend win over Wellington before tumbling to the ground with cramp taking a quick single.
No Watling confirms Tom Blundell gets an opportunity to back up from his fine debut in the first West Indies test. At the Basin Reserve, he became the first New Zealand wicketkeeper to score a century on debut, an unbeaten 107.
His glovework was generally tidy although he did let one ball fly beneath his gloves for four byes from spinner Mitchell Santner.
New Zealand coach Mike Hesson said although Watling is making good progress ''it's slow progress".
"He can obviously bat, he can move in the field, probably not as freely as he'd like and he's unavailable from a keeping perspective. It's a shame."
Hesson avoided the question of whether Watling would have come back for Tom Blundell, who made a century on debut at the Basin Reserve.
"We've always shown a lot of confidence in the incumbents. BJ has been a world class performer over a long period of time for us.
"Tom asked us a really nice question and showed he deserves more opportunities in time. It's not a question we need to answer at this stage, we're just delighted at how he went."
Hesson hinted Southee would come back into the test team, after missing Wellington for personal reasons.
"He played for ND [on Sunday], he's feeling good and has a really nice record for us in Hamilton so it's good to have him back."
New Zealand second test squad: Kane Williamson (c), Jeet Raval, Tom Latham, Ross Taylor, Henry Nicholls, Mitch Santner, Colin de Grandhomme, Tom Blundell, Tim Southee, Neil Wagner, Matt Henry, Lockie Ferguson, Trent Boult.
