The water district served the museum with a lawsuit citing eminent domain to put a 3,400-foot-long sewer line on a 2.4-acre piece of the 289-acre sanctuary.
The water district and the museum negotiated for months on where the underground sewer line would go and how much it would cost, but the two sides couldn't come to an agreement.
"The next step is to enter into eminent domain through the legal process," said Denise Hickey, North Texas Municipal Water District spokeswoman.
Hickey said the water district chose the piece of land because it was the most economical and would cause the least disruption to homeowners in the area.
But museum officials said they are worried about the disruption to the rare species of plants and animals that call the preserve home.
"There are several species of plants that that's the only place they are found on the whole sanctuary," said Roger Sanderson, a wildlife biologist. "They're just going to come in and dig a big trench and put in their pipe and fill it again with soil. Well, then all of a sudden, all that soil is disturbed. The species that were there will probably never be there again."
"We want to restore the property to the way it was found before we went into the installation of the pipeline route," Hickey said.
Sanderson said once the land is disturbed, it may never be the same again. He said noise from construction and toxic gases from the sewer line could scare animals away and they may never return.
Both sides said they hope to come to an agreement out of court.
The water district hopes to begin construction in December.