Police on scene say a white sedan carrying three minors was headed south when it was struck by the truck on Old Highway 30.
"We are still investigating the crash, but it looks like the car failed to stop at the stop sign or failed to yield from the stop sign pulling out on to the roadway, and was struck in the driver-side doorway by the manure truck," said Sgt. Jason Kagle of the Idaho State Police.
The crash killed the driver, a 17-year-old girl, and her 6-year-old sister.
The other passenger, an 11-year-old, was flown to a Boise hospital with unknown injuries.
The driver of the manure truck was not injured.