The area drained by the Whitewater River is part of the larger endorheic Salton Sea drainage basin.

Initially called Agua Blanco by early Spanish explorers,[14] and later translated into English as white water, the river received its name for its milky appearance created by the silicate and lime sediments it carries.

The Whitewater River has three significant tributaries: the North, Middle, and South Forks, all within the Sand to Snow National Monument.

Below the confluences, the arroyo is at least 0.5 mi (0.80 km) wide, paved with accumulations of boulders, gravel, and sand brought down by floods and brushy except in stream channels cleared by floodwaters.

The Pacific Crest Trail (PCT) enters the arroyo from the north and follows it downstream to a trailhead at the Whitewater Preserve, owned by The Wildlands Conservancy.