The Juaneño or Acagchemem Native Americans have lived in the Bell Canyon area for almost 10,000 years, from archeology at the San Dieguito complex.

Much of Bell Canyon was purchased by Eugene Grant Starr in the late 1920s, creating a large parcel of undeveloped land that became the National Audubon Society's 'Starr Ranch' in 1973.

A wide and braided watercourse flowing through an alluvial valley, Bell Canyon Creek remains much like its original state before the Spanish arrival, although with the development of Coto de Caza and nearby communities it has seen increased urban runoff, which does not often reach San Juan Creek in the form of surface water, but contaminates the local groundwater.

Work was begun in 2005 to remove polluted water from two Bell Canyon tributaries that flow through residential areas on the west side of the watershed.

Several pumps were installed on Dove and Tick Creeks in 2005 to remove excess surface water flow and feed the urban runoff into a reclaimed-water system.

The creek then trends southwards through a widening and shallowing valley for some 4 miles (6.4 km) before Crow Canyon enters from the left at RM 4.5 (RK 7.2).

Below the confluence with Bell Canyon, San Juan Creek flows 14.7 miles (23.7 km) further before emptying into the Pacific Ocean at Dana Point.

Rainfall exceeding 80 inches (200 cm) per year changed the slow-moving streams of the South Coast to powerful rivers that eroded deep channels into their floodplains to maintain equilibrium with the dropping sea level.

[7] The Wisconsinian era lasted from 70,000 to 10,000 years ago, and by the end of that period, climate changed to its present state and Southern California rivers reverted to small seasonal streams.

This riparian area consists of plentiful undergrowth bordering and near the stream, and many trees including the California Sycamore (Platanus racemosa), Fremont Cottonwood (Populus fremontii), and Coast live oak (Quercus agrifolia).

However, non-native invasive species of plants carried into lower Bell Canyon Creek from its tributaries, such as Periwinkle (Vinca major) and Ivy (Hedera spp.