The lower section of the creek flows through three incorporated cities and is moderately polluted by urban and agricultural runoff.

Acjachemen and Payómkawichum people lived along the perennial stream in settlements and hunting camps for 8,000 years before the invasion of Spanish colonization.

Local legend attributes a Franciscan missionary friar traveling with the Gaspar de Portolà Expedition in 1769 for the story that a blunderbuss was lost in the upper canyon by the creek, and so the naming of the area.

In its natural state, Arroyo Trabuco supported one of the most significant steelhead trout runs in Orange County, and birds, large mammals, and amphibians still flourish in riparian zones along its undeveloped portions.

[9] After entering the city limits of Rancho Santa Margarita, the creek flows southwest through the long, narrow wilderness preserve of O'Neill Regional Park.

[10][11] Still steadily bending southwards, Arroyo Trabuco is joined by Tijeras Canyon Creek from the left bank, then passes under a high bridge for Oso Parkway and leaves the southern boundary of the regional park.

[13] Passing into the northernmost extreme of San Juan Capistrano, it is joined by its largest tributary, Oso Creek, from the right.

[citation needed] Geologically the present-day Arroyo Trabuco basin did not exist as early as the end of the most recent Ice Age.

[18] As the Santa Ana Mountains rose, Arroyo Trabuco first formed as a canyon cut into the southeastern part of the range.

Arroyo Trabuco and other streams along the Orange County coast became powerful rivers that cut their way through the San Joaquin Hills.

[19] This changed climate did not last, and by the time it had ended, several enormous canyons had been cut through the 600-to-1,000-foot (180 to 300 m) high San Joaquin Hills.

Because of the enormous erosion channels carved out by the Wisconsinian-era rivers, the creeks now flow on broad and deep beds of sediment that have filled these canyons.

[19] The Arroyo Trabuco watershed, especially the Oso Creek subwatershed, has been severely affected by suburban development.

[25] Lower Arroyo Trabuco still supports some riparian zones, but they have decreased in health because of the introduction of urban and agricultural runoff.

Because of extensive modifications—affecting the stability and water quality of the creek—steelhead no longer migrate to the upper reaches of the Arroyo Trabuco watershed.

A project was proposed in 2005 to build a fish ladder into a concrete drop structure in Arroyo Trabuco that blocks steelhead passage.

$1.2 million was allocated by the California State Wildlife Conservation Board in 2005 to fund the project, but it has not been begun.