From the river they were blazing a new road west since the previous trails were suitable only for pack trains not for wagons. Zunis guided them for part of the route and led them to better river crossings. They also passed through the petrified forest area in northeast Arizona. The geologists were fascinated by the phenomena. From there they went west to the San Francisco mountains. They explored the volcanic cinder cones and lava caves.
Whipple discovered that the previous Sitgreaves trail map was incorrect about where the Bill Williams Fork entered the Colorado River. This caused him to go several days north out of his way. Whipple finally found the Big Sandy and followed it to the Colorado River. At that time several wagons had to be abandoned. Even some of their instruments had to be left behind.
When they reached the Colorado River on February 20, they traded with some Mojave Indians for much needed food. These Indians helped them locate a good crossing of the Colorado River near modern-day Needles, California. Several boats capsized, dumping much of their kitchen utensils. All the expedition notebooks were dumped into the river, but were saved by their Indian helpers. They also nearly lost a herd of sheep, when they became entangled in their lead. Their Indian friends once again saved the day. The Mojave also guided the expedition through the Mojave desert.
Whipple obtained an extensive list of their vocabulary. The area did not have much water and they lost quite a few mules in this stretch. They split the party into three groups so that watering holes could refill by the time the next group arrived. On March 13 they reached the Mormon Trail, a route from Salt Lake City to San Bernardino, California. They decided not to go to San Bernardino but headed directly west to Los Angeles. Much of the army escort led by Lt. Tidball left the expedition here to go to the garrison at San Diego.