Durst, 71, also faces a potential federal weapons charge, possession of a firearm by a felon, over the same gun allegedly discovered in his hotel room during his arrest. Durst pleaded guilty in 2004 to a previous federal weapons charge.
The circumstances surrounding the search of Durst's hotel room have come under scrutiny, as Durst's attorney, Dick DeGuerin, argued in a previous court hearing that they were done illegally.
Durst appeared shackled in a New Orleans court today and entered his plea on the state charges after DeGuerin whispered in his ear, according to The Associated Press.
"I am not guilty, your honor," he said, according to the AP. Asked if he was pleading not guilty to both charges, Durst said, "Yes, your honor."
After the court scheduled a May 7 evidentiary hearing, DeGuerin told reporters that Durst's team would be in federal court this afternoon over the potential federal charge.
"I feel like we’re being tag-teamed," DeGuerin said, "and I feel like we’ve got to be in California where the main case is so we can try the case."
Durst's arrest on the murder charge came just before HBO aired the final episode of a multi-part documentary featuring interviews with Durst, "The Jinx: The Life and Deaths of Robert Durst," in which Durst was confronted with evidence relating to Berman's murder and then recorded making possibly incriminating statements over an open microphone while in the bathroom.
Durst is being held without bail at a Louisiana state prison.
ABC News' Meghan Keneally contributed to this report.