The Mounties say 32-year-old Michael Kuntz died instantly when struck by pieces off the 'copter, which was running at the time.
His body was found in 1.5 metres of water near the sunken chopper.
Frank O'Connor piloted the Bell 206 which was leased from Aero Arctic by Environment Canada, police say.
Kuntz and 41-year-old Danny Dube, two Environment Canada employees, were conducting water surveys about 175 kilometres north of Yellowknife.
Both were nearby on the ice when the helicopter broke through the surface, which was 15 centimetres thick, according to RCMP.
O'Connor escaped the chopper, but he and Dube were soaked. They made their way to shore where they called for help with a satellite phone.
RCMP Const. Mike Chauvin said the thickness of the ice and stormy weather may have played a role in the accident.
"The six-passenger helicopter weighs in excess of 3,000 pounds," he said. "I know a small aircraft requires at least 10 inches (25 cm) of ice to land."
"He (O'Connor) may have landed on ice that was that thickness before without any problems," he said. "You can have soft ice. And that's a question the safety board will have to answer."
** The RCMP, coroner andThree helicopters flew to the scene. Environment Canada personnel in Yellowknife, who were the first to receive the call for help, also helped with the rescue.
Dube and O'Connor weren't injured, but they were transported to Yellowknife Stanton Hospital for overnight observation.
Yellowknife RCMP are assisting the coroner in the investigation.
The Transport Canada Safety Board has been notified and will also conduct an investigation.