While Bonita is politically designated as an unincorporated community, bounded by the incorporated cities of Chula Vista, San Diego, and National City the community of Bonita is more closely associated with the geography of the Lower Sweetwater Valley. Thus considered, Bonita occupies about a five mile stretch of the Sweetwater River, its valley, and surrounding hills on either side, bounded upstream (east) by the Sweetwater Reservoir, and downstream (west) effectively by Interstate 805. The community crosses west of I-805 -- an area less than 160 acres -- reaching as far south and west as East H Street and Hilltop Drive. Its northern boundary is State Route 54 and its southern extent reaches approximately one mile south of the river.

The climate in Bonita is a combination of the coastal and inland valley climates of San Diego County. Warmer (and sunnier during the May Gray and June Gloom periods) than areas directly adjacent to San Diego Bay or the coast, but not as hot as inland valleys such as El Cajon, or even nearby Spring Valley. In summer, Bonita's climate is pleasant.