As the troopers approached the Indian camp in the early morning darkness at 6:00 a.m., they found the Shoshoni warriors entrenched behind the ten-foot eastern embankment of Beaver Creek (afterwards called Battle Creek). The Volunteers suffered most of their twenty-three casualties in their first charge across the open plain in front of the Shoshoni village. Colonel Connor soon changed tactics, which resulted in a complete envelopment of the Shoshoni camp by the soldiers who began firing on the Indian men, women, and children indiscriminately. By 8:00 a.m., the Indian men were out of ammunition, and the last two hours of the battle became a massacre as the soldiers used their revolvers to shoot down all the Indians they could find in the dense willows of the camp.

Approximately 250 Shoshoni were slain, including 90 women and children. After the slaughter ended, some of the undisciplined soldiers went through the Indian village raping women and using axes to bash in the heads of women and children who were already dying of wounds. Chief Bear Hunter was killed along with sub-chief, Lehi. The troops burned the seventy-five Indian lodges, recovered 1,000 bushels of wheat and flour, and appropriated 175 Shoshoni horses. While the troops cared for their wounded and took their dead back to Camp Douglas for burial, the Indians' bodies were left on the field for the wolves and crows.

Although the Mormon settlers in Cache Valley expressed their gratitude for "the movement of Col. Connor as an intervention of the Almighty" in their behalf, the Bear River Massacre has been overlooked in the history of the American West chiefly because it occurred during the Civil War when a more important struggle was taking place in the East. Of the six major Indian massacres in the Far West, from Bear River in 1863 to Wounded Knee in 1890, the Bear River affair resulted in the most victims, an event which today deserves greater attention than the mere sign presently at the site.