Perchlorate from military, industrial, and legacy agricultural sources is present within an alluvial aquifer in the Rialto-Colton groundwater subbasin, 80 km east of Los Angeles, California (USA). The area is extensively faulted, with water-level differences exceeding 60 m across parts of the Rialto-Colton Fault separating the Rialto-Colton and Chino groundwater subbasins. Coupled well-bore flow and depth-dependent water-quality data show decreases in well yield and changes in water chemistry and isotopic composition, reflecting changing aquifer properties and groundwater recharge sources with depth. Perchlorate movement through some wells under unpumped conditions from shallower to deeper layers underlying mapped plumes was as high as 13 kg/year. Water-level maps suggest potential groundwater movement across the Rialto-Colton Fault through an overlying perched aquifer. Upward flow through a well in the Chino subbasin near the Rialto-Colton Fault suggests potential groundwater movement across the fault through permeable layers within partly consolidated deposits at depth. Although potentially important locally, movement of groundwater from the Rialto-Colton subbasin has not resulted in widespread occurrence of perchlorate within the Chino subbasin. Nitrate and perchlorate concentrations at the water table, associated with legacy agricultural fertilizer use, may be underestimated by data from long-screened wells that mix water from different depths within the aquifer.