The owner, Burak Akbay, and three others, including the executive in charge of the website, Mediha Olgun, are accused of links to the movement led by Islamic preacher Fethullah Gulen blamed for last year's failed coup, Anadolu news agency reported.
The fiercely anti-government and ultra-secularist daily whose name means "spokesman" is one of the country's bestselling papers. Its slogan is: "If #Sozcu is silent, Turkey will be silent."
Istanbul prosecutors issued four arrest warrants including correspondent Gokmen Ulu and Yonca Kaleli, a finance executive, CNN Turk broadcaster said.
The daily confirmed Olgun and Ulu's detention on its website this evening while CNN Turk said Akbay was in London.
More From This Section
"We have fought against terrorist organisations, FETO. As journalists, we have written the truth when they have committed large wrongs against this country," Ulu told reporters earlier in the day before he was taken into custody.
Istanbul prosecutor Irfan Fidan confirmed the operation into "Sozcu's executives", saying "there are warrants, there are detentions" without giving details.
Sozcu's lawyer Ismail Yilmaz denied arrest warrants had been issued, saying warrants had been issued to seize and search their belongings.
And Yilmaz suggested earlier Olgun's detention could be in connection with another investigation, the private Dogan news agency reported.
The four are accused of "committing crimes on behalf of an armed terror organisation", referring to the Gulen movement, CNN Turk reported.
Turkey refers to the movement as the "Fethullah Terrorist Organisation" (FETO), but Gulen vehemently denies ordering the coup and the movement denies any terror charges.
The accusations levelled at them include attempted "assassination and real attack of the president" and involvement in an "armed rebellion against the government", Anadolu said.
The article in question revealed details of where President Recep Tayyip Erdogan was on holiday in the upmarket Aegean resort of Marmaris, CNN Turk said, and had images of his hotel.
Sozcu is the second daily to be targeted after another leading opposition newspaper Cumhuriyet saw 20 staff members charged under the state of emergency imposed following the attempted putsch.