Maximum discharge along the river is currently at the reporting a streamflow rate of cfs. This is also the highest stage along the Babocomari River, with a gauge stage of ft at this location. This river is monitored from 1 different streamgauging stations along the Babocomari River, the highest being situated at an altitude of ft, the .
The Babocomari River is a major tributary of the upper San Pedro River in southeastern Arizona. The river begins in the Sonoita Basin near the community of Elgin, Arizona, and flows eastward for approximately 25 miles (40 km) before merging with the San Pedro, just south of the Fairbank Historic Townsite in the San Pedro Riparian National Conservation Area. The Babocomari drains an area of about 310 square miles (800 km2), including the northern Huachuca Mountains, the northwestern Canelo Hills, and the southern Mustang Mountains, and is one of three drainages of the Sonoita Basin, the other two being Sonoita Creek and Cienega Creek. Vegetation consists of riparian trees along the main channel and small marshy grasslands.