Police found the bodies Sunday night after the girl's mother called 911.
The identities of the man and the girl have not been released.
Commander Jeff Satur with the Longmont Police Department tells 9NEWS the father had been watching the toddler since Friday night because the mother went on a camping trip. The couple had been recently separated, according to a neighbor.
Satur said when the mom was driving to pick up her daughter, the daughter's father wasn't answering up the phone. She got to the house and no one answered the door.
The woman's teenage son eventually was able to get the key to the home, but at that point, according to police, the woman wasn't comfortable going inside. She called 911.
Police entered the home, located in the 1200 block of Red Mountain Drive, using the key about 5 p.m. Sunday night.
Investigators say they found a lengthy suicide note but are not yet able to reveal what the note said.
"I'm absolutely shocked," said a neighbor who did not want to be identified, "In my opinion, there is no way he could've done this. He loved that girl so much. It was his dream to have her. He was a really nice guy. They were a great family. They were great friends for 10 years. This makes no sense. Can't comprehend it."
Longmont Police say the couple had lived in the home since 2004.
Satur said the mother of the 3-year-old told police her husband had been suicidal earlier in the year.
Both people had been shot with a revolver registered to the father, according to police.
"These cases, child abuse cases, tug at your heart because we all have kids," Satur said. "[It] just makes you thankful your kids are safe. It is very hard to investigate these cases."
Satur said investigators have so far been unable to find any prior records of being called to this home for any other reason.
9NEWS has learned the name of the father, but has decided not to release his name until police notify his family.
9NEWS learned the father was arrested in June for felony theft charges after allegedly selling Home Depot gift cards without money on them on Craigslist for $1,400.
One neighbor called 9NEWS on Monday to say the neighborhood in general is very concerned for the welfare of the 3-year-old's mother.
"We all hope she's doing ok," she said.
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