A spokesman for the Saskatchewan Ministry of Environment said all three suspects, whose names have not been released, were arrested Saturday morning in a small Saskatoon-area community.
Search warrants were also carried out at two of the individuals' residences.
Gary Harrison, manager of the department's special investigations unit, said provincial and federal wildlife officers and the RCMP were also able to pin down the location where the video was shot.
"It's close to the community that the arrests were made in," he said.
The men, who are all in their early 20s, will appear in Saskatoon provincial court on Monday to face a variety of charges under provincial and federal wildlife laws.
Harrison won't speculate on the motive for the shooting. He also said more investigation is needed of the area where the video was shot.
"Anybody who has watched the video knows that some birds have been killed and we really don't know how many that was," he said.
The environment ministry said the content of the video led to a significant number of calls to poacher tip lines in both Saskatchewan and Alberta - a number Harrison calls "unprecedented."
The video depicts two of the men firing at the ducks while the third captures their glee on camera. Police and provincial authorities launched an investigation late last week, soon after it appeared on YouTube.
Harrison said the video is very unusual.
"When I started we didn't have the Internet and YouTube. I haven't seen one that's been posted like this and had the killing of the birds in a media form like that," he said.
The video sparked widespread public anger and prompted the Toronto-based Humane Society of Canada to post a reward of $1,000 for information leading to the arrest of those shown in the Internet posting.
Society executive director Michael O'Sullivan said the organization also got calls from people who wanted to help and they were directed to tip lines in both western provinces. O'Sullivan said he is pleased to hear of the arrests.
"I would like to commend all the members of the public who provided information. Canadians take cruelty to animals very seriously and they want to help out as best as they can," he said.
All three men have been released prior to their first court appearance.