Two weeks ago the EPA declined the marine consent citing "uncertainty around the scope and significance of the potential adverse environmental effects".
TTR then had 15 working days to appeal.
Chairman of the anti-mining group KASM, Phil McCabe, said the EPA decision had been comprehensive and had "appealed for them [TTR] not to appeal".
But he wasn't surprised by the company's move.
"We wouldn't expect them to run away from a $60 million investment," Mr McCabe said.
He said KASM would continue to fight plans to mine the seabed. "We'll see what grounds they appeal upon, we'll do our work and see how we'll respond."
Whanganui MP Chester Borrows reiterated his view that if the environmental concerns could be allayed there was no reason the project shouldn't go ahead.
"I'm a supporter of it as long as it stacks up," he said. "I'm quite happy they're going through the process of appeal."
TTR, which successfully applied for a mining consent earlier this year, expected the High Court to deal with the issue within six months. The company wants to extract up to 50 million tonnes of iron-rich sediment per year and process the sediment aboard an integrated mining vessel. From that, about five million tonnes of iron ore concentrate will be exported a year.