The International Justice Mission confirmed that the two bodies found were of staff lawyer Willie Kimani and taxi driver Joseph Muiruri.
The body of activist Josephat Mwenda, whom Kimani was representing, is still missing, the mission said in a statement.
The bodies were found in the Ol-Donyo Sabuk River northeast of Nairobi. A third body slipped back into the river.
Human rights groups have said the men were abducted on June 23 while coming from court, where Mwenda faces several charges including narcotics possession.
More From This Section
The groups say the charges were trumped up by a policeman after he shot Mwenda without provocation in April 2015. Mwenda had said he received threats after he reported the officer to the Independent Police Oversight Authority.
In December, the officer who shot Mwenda picked him up from his home and charged him with driving a motorcycle without a helmet and other issues, the rights groups said. The groups said Mwenda was still nursing his bullet wound and couldn't drive.
Police in 2015 were involved in more than a third of the crime reported to police, the government's economic survey said last month.