The naked body of Michael Gerard Hampson (53) – known as Gerard – of Northland Road in Derry was found on January 9 that year close to Toomebridge.
The inquest previously heard from his family that he had a “pathological fear” of water.
He had been wanted by police for questioning over a kidnapping incident in Mullingar, Co Westmeath, in April 2007.
The inquest heard some had expressed concern about Mr Hampson “talking”.
Coroner Joe McCrisken found Mr Hampson was likely to have been drowned by others in the Moyola River in late 2007.
Delivering his findings in Omagh Courthouse on Wednesday following the inquest, Mr McCrisken said there are a “great many improbabilities, inconsistencies and impossibilities surrounding Mr Hampson’s death”.
He added: “I find it highly improbable that Gerard Hampson died by natural causes, suicide or accident.
“It seems to be the truth must be that Mr Hampson died as a result of the actions of a third party or persons.
“I am satisfied on balance that Mr Hampson died as a result of drowning, probably on the Moyola River on November 30, 2007.”
He said he believes it is likely his clothes had been removed by a third party to potentially remove any forensic link.
Mr McCrisken made reference to evidence given to the inquest by Mr Hampson’s niece, who recalled seeing him at the end of November 2007 and noted he seemed “on edge”. She said he did not know when asked if he was safe.
“According to Mr Hampson’s niece, her uncle told her, ‘there are boys after me and I don’t know where to go’,” the coroner said.
Inquest rules in Northern Ireland prevent coroners from giving any opinion on civil or criminal liability.
There were no referrals made to the Public Prosecution Service.
Mr Hampson was described as a former bricklayer who had struggled with alcoholism and some mental health difficulties, and could be considered a “vulnerable man”.
He had spent time in custody as a republican prisoner during the 1970s.
Mr McCrisken paid tribute to Mr Hampson’s family for their patience, adding they had waited too long for inquest findings.
“They have listened to the evidence with respect and shown great respect for this entire process,” he said.
“Grieving families are entitled in my view to have an answer to the most human questions – what happened to my loved one? I hope these findings provide at least some answers to this question.”
In a statement, the Hampson family thanked the coroner for his findings but said many of their questions “remain unanswered”.
They welcomed the conclusion that Mr Hampson did not take his own life.
“This brings us great relief,” they said.
“It has taken 14 years for our family to have some answers about how our father died, and although we still have questions that may never be answered, we feel that today marks a degree of justice and closure.
“Our father Gerard, known to his friends and family as ‘Shorty’, was loved deeply by all who knew him. He had an amazing sense of humour and was adored by his grandchildren.
“Today does mark a victory for our family. We never believed that our father took his own life, and the coroner has examined the evidence over the court of this inquest and has reached the same conclusion. This brings immense relief to our family and draws a line under the innuendo and suspicion around his death.
“During that time our family have had to fight every single day to find out the truth about what happened to him. Today we have some answers.”
The family also criticised the initial PSNI investigation, which was examined by the Police Ombudsman.
Responding, assistant chief constable Mark McEwan said the initial investigation “fell far below the standard that Mr Hampson and his family deserved”.
“I again wish to put on record how sorry I am. We acknowledged and accepted that there were lessons to be learned from this case,” he said.
“The 2016 Ombudsman report recommended disciplinary sanctions against 10 officers.
“After careful consideration by a senior officer, it was agreed that there was a requirement for disciplinary sanctions against eight officers and these have since been imposed.”
He said while two people were arrested around Mr Hampson’s death in 2016 and 2019, and while files were submitted to the Public Prosecution Service, convictions were not secured.
He added: “At this point, all our investigative lines of enquiry have been exhausted, however we would urge anyone with any information regarding this case to come forward.”