The California Department of Water Resources includes San Juan Creek in the San Juan Hydrologic Unit, which includes the coastal watersheds of Aliso Creek, Salt Creek, Prima Deshecha Cañada, Segunda Deshecha Cañada, and San Mateo Creek, which share a similar range of elevations and climate. Elevation in the Hydrologic Unit ranges from sea level to at Santiago Peak (the headwater of Holy Jim Creek, a tributary of Arroyo Trabuco). The climate is Mediterranean, with hot, dry summers and cool, wet winters. Almost all the precipitation occurs between October and April; the average rainfall is , although mountain areas often receive higher amounts. San Juan Creek receives extra runoff from agriculture, urban areas, and other human sources, resulting in unnatural dry season flows that carry trash, heavy metals, oils, pesticides and fertilizer into the creek. The heaviest source of pollution is Oso Creek. Michael Hazzard, a Southern California environmentalist, said after diving into Upper Oso Creek Reservoir: I spent three days diving to retrieve an outboard motor and my skin broke out in hives and boils and my gallbladder suffered and I later had six operations over a 2​1⁄2-year period.