Kem Ley's death comes amid rising political tensions between veteran Prime Minister Hun Sen and an opposition hoping to challenge his grip on power at local elections in 2017 and national elections in 2018.
The Phnom Penh city court charged Chuop Somlap, 38, with the premeditated murder of Kem Key, 46, the founder of grassroots advocacy group "Khmer for Khmer", deputy prosecutor Ly Sophana told reporters.
He was also charged with the illegal possession of a weapon and another unidentified person was charged with the illegal sale of a weapon to Chuop Somlap, Ly Sophana said.
Chuop Somlap was arrested shortly after the shooting on Sunday. In a police video he claims to have killed the popular political commentator over a $3,000 debt.
Members of Cambodia's opposition and activists have been jailed in recent months on charges they say were trumped up by the government as part of a crackdown to mute critics ahead of the elections.
Many of Kem Ley's supporters said the murder was political and were sceptical of the reason given for the killing.
Kem Ley's family said the activist did not owe money, adding that they now feared for their safety.
"If I continue to live in Cambodia, it's not safe," Kem Ley's wife Bou Rachana said.
While Chuop Somlap's wife said her husband was a poor, unemployed man and would not have had such a large amount of money to lend. "He has never had that much money," she said.
Kem Ley was a frequent critic of Hun Sen, whose more than 30 years grip on power has been challenged by the rise of the opposition Cambodia Nation Rescue Party (CNRP).
His most recent critique was a commentary on a report by anti-corruption pressure group Global Witness, which accused the prime minister and his family of having amassed $200mn in business interests.