He isn't talking about the wave, he's talking about the time it'll take to drain the engines of water and return to space, noting that they're in a gravitational well so large that time on the planet is passing much faster than on the Endurance:
The novelisation explains it a little better than the script;
“How bad?” he asked, thinking that he most likely didn't want to know.
“Every hour we spend on that planet will be maybe…” She did the mental
computations. “Seven years back on Earth.”
“How long to drain, Case?” he asked.
“Forty-five to an hour,” the robot informed him.
Cooper shook his head and uncoupled his helmet. The cabin was pressurized. Everything smelled wet, but it didn't smell like seawater or a pond. It smelled like distilled water that had been dumped on hot rocks—a mineral scent, but not salt.
“The stuff of life, huh?” he said. “What’s this gonna cost us, Brand?”
“A lot,” she said. “Decades.” Her voice was flat.
Cooper felt like he couldn't breathe. Decades. Tom and Murph were adults already. How old? It seemed impossible. He rubbed his face, trying to comprehend it. He watched the wave go, knowing there would be another, and soon.
As it happens, in the end it doesn't actually take them as long to leave the surface as they first feared, evidently due to Cooper's innovative idea of blowing air through the engines to clear the water.