The pair had been traveling in the Javari Valley, in the far western side of the Brazilian Amazon, before they were killed.
The boat was located at a depth of about 20 meters (over 65 feet), capsized with six bags of sand to make it difficult to float, at a distance of 30 meters from the right bank of the Itacoaí River, near the Cachoeira community, according to a report from the Civil Police.
A suspect arrested on Saturday pointed authorities to the location of the speedboat.
Three suspects have so far been arrested for the murders, Brazilian Federal Police confirmed on Sunday, and another five are being investigated for their alleged involvement in hiding the corpses of the victims.
"Investigations continue to clarify all the circumstances, the reasons and those involved in the case," the police said in a statement.
Phillips and Pereira disappeared while conducting research for a book project on conservation efforts in the region, which authorities have described as "complicated" and "dangerous," and known to harbor illegal miners, loggers, and international drug dealers.
They had reportedly received death threats just days prior to their disappearance.
Their case has drawn global attention to the perils often faced by journalists and environmental activists in Brazil.
Between 2009 and 2019, more than 300 people were killed in Brazil amid land and resource conflicts in the Amazon, according to Human Rights Watch, citing figures from the Pastoral Land Commission, a non-profit affiliated with the Catholic Church.
And in 2020, Global Witness ranked Brazil the fourth most-dangerous country for environmental activism, based on documented killings of environmental defenders. Nearly three quarters of such attacks in Brazil took place in the Amazon region, it said.