Akin Atalay was taken into custody at Istanbul's airport after arriving from Germany, said Cumhuriyet, which also saw nine of its staff arrested last week.
The paper has in recent years taken a strong line against President Recep Tayyip Erdogan's ruling Islamic-rooted Justice and Development Party (AKP).
Atalay was targeted by a warrant that was part of a probe into "terrorist activities", and was ushered into a police vehicle that was waiting for him on the tarmac.
Some 35,000 people have been arrested and tens of thousands more have lost their jobs -- including military officers, judges, teachers, civil servants and journalists -- in a sweeping crackdown in the wake of the failed July bid to oust Erdogan.
The news comes as nine MPs from the opposition pro-Kurdish People's Democratic Party (HDP), including its co-leaders Selahattin Demirtas and Figen Yuksekdag, were detained last week pending a trial on terror charges expected to begin Friday.
Nine of the paper's staff, including its current editor-in-chief, were remanded in custody last weekend pending trial after raids that have added to growing international alarm about media freedoms in Turkey.
The paper's exiled former editor-in-chief, Can Dundar, fled to Germany earlier this year while appealing against a near six-year jail term for revealing state secrets.
Among the nine to be held ahead of trial were Cumhuriyet's editor-in-chief Murat Sabuncu, celebrated cartoonist Musa Kart and influential anti-Erdogan columnist Kadri Gursel.
However, columnists Hikmet Cetinkaya and Aydin Engin were released on bail on health grounds and because of their age. Two other suspects from the newspaper's accounting department were released without charge.
The suspects are charged with links to the Kurdish militant Kurdistan Workers Party (PKK) and the movement of US-based preacher Fethullah Gulen, blamed for the failed coup bid. Gulen denies the accusations.
Dundar was sentenced by a Turkish court in May to five years and 10 months in prison for a story about a shipment of arms intercepted at the Syrian border, which had prompted a furious Erdogan to warn Dundar he would "pay a heavy price".
Amid mounting fears for Turkish press freedom, on Tuesday the Turkey representative for Reporters Without Borders (RSF) and two other campaigners went on trial charged with making terror propaganda for Kurdish militants.