Most of Blue Oak Ranch Reserve (BORR) lies within the Upper Sonoran Life Zone. Approximately two-thirds of the site is drained by tributaries of Arroyo Aguague, itself a tributary of Coyote Creek (via Penitencia Creek), which flows into southern San Francisco Bay.

The bowl-shaped Arroyo Aguague catchment area is characterized by steep wooded slopes and meadows, as well as open flats dotted with oaks and coyote brush. The precipitous Arroyo Hondo is heavily wooded on north- and east-facing slopes, while western and southern exposures consist of open grassland or dense chaparral patches.

Streams on the ranch support healthy stands of riparian vegetation in addition to aquatic species. They are important habitat for migratory birds and may be migratory corridors for numerous aquatic and terrestrial animal species.

At least 73 vascular plant families are found at BORR, almost 80 percent of which are native. Plant communities include blue oak woodland, valley oak woodland, black oak woodland, coast live oak woodland, riparian forest, chamise chaparral, Diablan sage scrub, nonnative annual grassland, wildflower field, and native perennial grassland. Four of these are threatened plant communities: valley oak woodlands, blue oak woodlands, wildflower field, and native perennial grasslands. Blue and valley oak woodlands have become quite rare in California, and few are protected from grazing and the encroachment of suburban development as they are at BORR.

Foothill pines occur only in the Arroyo Hondo and on the slopes above its confluence with North Creek. Chaparral patches occur on many south-facing and some west-facing slopes. Grasslands are mainly dominated by exotic annuals, but some native perennial grasses are present.