Draining a watershed of 8.2 square miles (21 km2), the lower portions of the stream were modified according to the local land uses, initially agriculture, and in the 1950s, suburban development.

This involved straightening of the stream and elimination of wetlands and the reclamation of the former Lake Mathilda at the lower western zone with landfill.

These and other plants such as Wake robins, Coast and Giant trillium, and slender false Solomon's seal blossom between clustered stems of shrubs and clumps of sword fern.

[4] The fact that these species normally grow in the shady understory of redwood and Douglas fir forests, has led to speculation that prior to the 5,000 year occupation of the Ohlone Indians, who likely burned off the area to promote the growth of natural food sources, that the upper San Pedro watershed may have been host to primordial conifer forests.

The three forks of the San Pedro and its Brooks Creek tributary provide critical spawning areas for steelhead trout (Oncorhyncus mykiss).

A year 2000 comprehensive study, in cooperation with the San Francisco State University Masters program reviewed the in-stream chemical, physical and biological qualities of the creek.

The dominated pollution was E. coli traced to avian sources, but also significant association with dogs, human, horse, raccoon and deer.

The improved culvert, in addition to a system of weirs and pools restored the ability of juvenile fish to travel upstream through this portion of the creek in 2005.