The largest rare earth element (REE) deposit in the United States is a carbonatite intrusion at Mountain Pass in the Mojave Desert, California. Despite a clear spatiotemporal association of alkaline silicate and carbonatite intrusions at Mountain Pass, a genetic model of their mutual formation has not been resolved. The Mountain Pass carbonatite has long been upheld as an example of a primary magmatic body, but recent work has suggested it could be fluid-derived. This study investigates the geochemistry of apatite and monazite grains from the alkaline silicate and carbonatite stocks and dikes of the Mountain Pass district, to elucidate the magmatic history of the intrusive suite and identify the role of fluids in rare earth element mineralization. Three apatite populations are identified in the alkaline silicate rocks. A primary magmatic apatite group supports intrusion of the stocks as separate pulses of magma derived from a spatially extensive metasomatized mantle source region. The second group implicates the role of a regional fluid that mobilized light rare earth elements from apatite grains. A minor group of inherited apatite cores, identified by low Sr and negative Eu anomalies, supports assimilation of crustal material in the formation of the intrusive suite. Analyses of monazite and apatite grains from the carbonatite orebody also reveal a mix of primary magmatic and metasomatic (fluid-related) minerals. Compositional similarities between primary phosphates in the carbonatite and alkaline silicate rocks support a genetic link between the intrusive suites. The presence of fluids regionally and within the carbonatite orebody indicates the Mountain Pass carbonatite should not be classified as a purely magmatic REE deposit.