Kawarau Jet had opposed the consent on grounds of river safety and radio communication compatibility.
However, Judge Newhook said the court had the impression Kawarau Jet's "conduct and refusal to co-operate remained motivated by trade competition", in his critical decision.
The judge said the case by Kawarau Jet was "characterised by evidence that lacked accuracy and credibility".
Kelly said although he had not yet read the decision in detail, there were regrets about how the case was handled - but "that's water under the bridge".
Kelly said the relationship between the two companies on the water was "totally amicable" and they had to work together.
Water Taxis co-director Neville Kelly said he was pleased with the outcome, although they were still out of pocket for earlier commissioner hearings.
"We just move on now. We've got consent for four boats and we're up to 34 trips a day and business is just getting better and better.
"There's no issues with radio ... and there's never been an issue with safety. If there was, I wouldn't be doing it."
Council spokeswoman Meaghan Miller said yesterday: "Clearly we're pleased with the decision. The costs awarded were the costs that we sought."
Asked if Kawarau Jet would appeal against the costs decision, Kelly said it was a matter for the board to discuss and members were out of town.