Waters, 40, was eventually extradited to Australia after his arrest in the Serbian capital in January 2018 and is on trial accused of conspiring to import a border controlled drug.
He has already pleaded guilty to attempting to possess the drugs, found inside steel beams in a shipping container the previous year.
Businessman David Campbell has pleaded not guilty to both charges.
Campbell told a NSW District Court jury he tried to track the shipping container down on behalf of a client when it went "missing", after police found drugs inside, and then became dragged into a conspiracy due to threats to his family.
In closing submissions to the jury on Monday, crown prosecutor Sean Flood alleged Waters was an influential figure in a drug trafficking syndicate.
Undercover police posing as criminals named Henry and Ivan, who had happened upon the container with almost a tonne of pure cocaine inside, lured Waters and Campbell to Serbia in an alleged attempt to retrieve it.
Waters was well involved in trying to make sure the doomed transaction would succeed, the prosecutor said.
Waters texted a high-ranking syndicate member, known as "Governor" among other names, to share what precautions were being taken ahead of a meeting in Belgrade with Ivan to exchange funds before the drugs would change hands in Perth.
If Ivan tried to call off the deal, he could be bundled into a van by men who were "all strapped, ready to roll", Waters assured.
"I've got 12 boys here, some of who are cops too, so I've got it all covered," Waters allegedly texted Governor.
Mr Flood told the jury there would be no reason for Waters to lie or put on an act in the messages, which were expected to never be read by authorities.
In group chats on encrypted devices used by the alleged conspirators, a username attributed to Waters provides planning and direction, and rustles up high-ranking figures and information from more exclusive discussions when required.
"Even before you look at the detail you can see Mr Waters is high up in the syndicate because he is being allowed to see what is going on in a number of areas," Mr Flood told the jury.
In addition to Governor, Waters also expressed familiarity with a second unidentified group chat participant known as MC, describing him as a "funny guy".
Waters described the trio as "all high strung, aggressive individuals."
"I'm the most level headed out of the three," he said.Â
Mr Flood has urged the jury to explore links in the evidence seeking to prove Waters was deeply involved in the conspiracy to import the drugs, not just possess them.
He also urged the rejection of Campbell's evidence about his involvement being under duress.
Campbell said he did not report threats because he had distrusted police since he was a child, blaming them for breaking up his family.
Another "major factor" was the AFP's response to a tip-off from the father of convicted Bali Nine heroin smuggler Scott Rush, who is spending his life in an Indonesian jail, Campbell said.
Former AFP commissioner Andrew Colvin said in 2015 the information provided was not shared with Indonesian authorities, but made no difference to their investigation and police were not in a position to make arrests before the Bali Nine left Australia in 2005.
The trial continues in front of Judge Phillip Mahony.
