Travers said during the first few runs, it was clear the heavier water would not "slosh" out of the sandy track, which erodes the banks and makes the water more buoyant.
Therefore, the drivers had to contend with more "choppy" waves.
"There was quite a few offs," Travers said.
Taking up time to removed beached craft meant the final playoffs were run as a Top 6 for each division, rather than progressing to the Top 3.
"The first four boats all came out the water," said Travers, who was waiting to go last with navigator son Shane as the fastest qualifiers.
Wellington's Ray Ferguson survived his run to post a reasonable 61.7s time, which had Travers confident as he had previously reached 61.2s.
However, there was near disaster after the first right turn coming back into a hard left.
"I thought it was going to come out, but I slid up and came back again," said Travers.
Carrying on, Travers still thought his near miss was going to cost him the Cup on time, but he and Shane were surprised when they reached the end to discover they had surpassed Ferguson by 1.6s.
Travers hopes the one-off cup victory can be the springboard into the remainder of the Altherm Window Systems New Zealand Jetsprint Championship season.
"We had a good run all day, didn't have to touch anything on the boat at all."
"We're sure it was the jet unit, not the engine, was the trouble. I'm 98 per cent sure we've got it sorted.
"Hopefully we give Ollie [Silverton] a bit of a hurry up if we can.
"Whanganui cleaned up, which was bloody excellent."
Wilson said before the event he wanted the other drivers to give the crowd a show by crash out, and that was what happened.
"I stayed in the water, because once you sit it out, that plays on your mind as well [in later laps].
"There was quite a few boats that were flipping out of the water."
Wilson also had the fastest time coming into the Top 6, and had considered Te Awamutu's Patrick Haden to be his biggest threat.
However, Haden had a navigation error and dropped out of contention, while Waitara's Daniel Reade posted a good time to ultimately finish third, and young Hastings driver Jakeb Simmons had a brilliant lap for second.
But Wilson and his navigator partner Amanda Wilson had it under control with a 65s final lap to claim the Stadium Cup, which includes to smaller replica cups that they get to keep when the big one is returned.
"Everything's as good as gold," Wilson said.
"We've got a bit of work to do before Waitara, and then hopefully we should be up there [in the standings]."
The Waitara round of the nationals will be on February 24.
