The decision also targeted 135 other online addresses including YouTube and DailyMotion videos, as well as the Twitter account of Kurdish member of parliament Oya Ersoy.
The court in Ankara said the decision - which followed a police request - would "protect... national security and public order", without explaining how.
Founded in Istanbul in 1997, Bianet is well-known in Turkey for its articles on human rights, violence against women and its exhaustive coverage of trials linked to freedom of expression. Its articles are published in Turkish, English and Kurdish.
"The decision has not even been transmitted to Bianet, we found out by chance," the site's lawyer, Meric Eyboglu, told AFP.
"We were able to confirm that the decision covers the entirety of the website - it will be totally blocked. The closure of the site could happen at any moment," she said.
An article on Bianet said more than 200,000 of its articles would be lost by the shutdown.
The local chapter of Reporters Without Borders (RSF) decried the decision as "scandalous" and "totally arbitrary", calling for it to be overturned.
Rights groups have regularly criticised the erosion of free speech in Turkey under President Recep Tayyip Erdogan, especially since a failed coup attempt in 2016 triggered a massive crackdown on government critics in the press and beyond.
Turkey is the only country apart from China to block Wikipedia, and was ranked 157th out of 180 countries for freedom of the press in the most recent RSF list.
