In Santa Rosa, the creek parallels Creekside Road, Cypress Road, and Hoen Avenue westward to Doyle Community Park, where it is joined by Spring Creek.

The upper reaches of Matanzas Creek have gradients of five to fifteen percent as the stream cascades down Sonoma Mountain.

[4] Matanzas Creek channel has been deepened 4 to 5 meters to minimize urban flooding where it flows through Quaternary alluvium of the Santa Rosa Plain for approximately 1 mile (2 kilometers) prior to confluence with Santa Rosa Creek.

[5] In downtown Santa Rosa, the creek passes through a 1,400-foot-long (430 m) culvert designed to allow maximum development of the city; however, this structure has impeded the spawning of anadromous fish in the upper Matanzas Creek.

A proposal was developed for retrofitting the structure with inflatable bladders that will allow fish to scale the fish ladder, while allowing pools to form, thus preventing low flow uniformly shallow depths.