Turkish police were frantically searching for other suspects linked to the man, who had undergone plastic surgery apparently to help conceal his identity. Authorities were also hunting for two squads of possible suicide bombers, reports said.
Meanwhile, Israel lifted a travel warning against visiting southern Turkey that was in place because the apparent al Qaeda threat was against Israeli tourists.
A statement from Israel's counterterrorism center said that due to efforts from Turkey's security forces, the threat level had dropped.
Defense lawyer Osman Karahan said his client, who was identified in the Turkish press as Lu'ai Sakra, was found with 1,650 pounds of explosives.
"He was planning to hit Israeli ships in international waters with these explosives," CNN-Turk quoted Karahan as saying.
Sakra shouted that he had no regrets after he was led handcuffed by police into the courthouse.
"I was going to attack Israeli ships," he said. And then in an ominous threat, he added: "If they come, my friends will attack them."
"I had prepared a ton of explosives," he also said in a barely audible voice. He spoke Turkish with an Arabic accent.
A statement from police headquarters said the suspect had an important position within al Qaeda and had undergone plastic surgery. The Hurriyet newspaper said Sakra had had plastic surgery several times, to change his appearance.
A Turkish police official said security forces were looking for other suspects linked to Sakra. Private NTV television said police were searching for two teams of possible suicide bombers.
Five cruise ships carrying some 5,000 Israeli tourists have been diverted from Turkish ports to Cyprus in recent days following intelligence reports that a terror attack was imminent.
Israel on Monday urged its citizens not to visit beach resorts on Turkey's Mediterranean coast before reversing the travel warning Thursday. Turkey is a top vacation spot for Israelis, and more than 300,000 visit each year.
In Israel, a security official said the Israeli travel warning will remain in effect due to a continued threat of attack.
The Istanbul court charged Sakra Thursday with membership in an illegal organization, defense lawyer Ilhami Sayan said. He refused to give any details, citing court regulations.