RSF representative Erol Onderoglu, rights activist Sebnem Korur Fincanci and journalist Ahmet Nesin were being tried at the main courthouse in Istanbul. They were initially arrested in June but then freed pending trial.
All three have been charged with making "terror propaganda" on behalf of the outlawed Kurdistan Workers Party (PKK) after guest-editing pro-Kurdish Turkish newspaper Ozgur Gundem.
Ozgur Gundem had invited guest editors to take control of the paper in a campaign of solidarity as it faced pressure from authorities.
One of the paper's columnists and board members, the internationally-renowned novelist Asli Erdogan, was arrested in the raid and has now been held for 82 days on charges of terror propaganda.
Onderoglu's detention on June 20 triggered international alarm over press freedom in Turkey but concerns have grown further as the authorities imposed a state of emergency in the wake of the July 15 failed coup.
Critics say that the state of emergency is being used against any opponent of Turkish President Recep Tayyip Erdogan and not just the suspected coup plotters.
Decrying the "extinction" of civil society in the country, he added: "The European ideal is fading away in Turkey."
Nine executives and journalists for the top opposition daily Cumhuriyet were sent to jail at the weekend on charges of links to terror groups that supporters say are laughable.
According to the Platform for Independent Journalism website, there are now 142 journalists behind bars in Turkey. Turkey is ranked 151st of 180 countries in the 2016 World Press Freedom index published by RSF.
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