The senior seamer missed New Zealand's innings and 67-run win at the Basin Reserve due to the birth of his child.
Southee returned for the opening round of the Ford Trophy and picked up three wickets in Northern Districts' five-wicket win over Wellington in Whangarei.
Canterbury seamer Matt Henry took Southee's place in the first test and took three second innings wickets with an impressive performance.
Southee (29) has taken 204 wickets in 57 tests and seems likely to return for the Hamilton test as a regular first choice pick.
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 last 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 Mitch Santner.
The spare players in the Wellington test squad, George Worker and Lockie Ferguson, are being released back to Central Districts and Auckland for tomorrow's second round domestic 50-over matches.
However Ferguson will rejoin the test squad on Thursday to prepare for the second test, which starts on Saturday.
The reason they were not released for the first round, after being left out of the first test was it was felt better they stay and train with the red ball, rather than dropping back to playing white ball cricket with their provinces.
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.
