It runs from runoff in the Presidio and Seacliff areas and underground seepage from springs that form Mountain Lake to the Pacific Ocean marking the division between Baker Beach and China Beach. Conservation and restoration efforts are under way to remove invasive vegetation and improve water flow, in addition to deculverting.
Lobos Creek is the Presidio's primary source of potable water. About a million gallons per day—half the average flow of the creek—is diverted to a water treatment facility in the Presidio.
Broken pipes also leak raw sewage into the creek, causing a pool at Baker Beach and Lobos Creek where children play to be the most contaminated in the Bay Area.