We determine the reflection polarity and exploit variations in P and S wave reflectivity and P wave amplitude versus offset (AVO) to constrain the origin of lower crustal reflectivity observed on new three-component seismic data recorded across the structural transition of the Colorado Plateau. The near vertical incidence reflection data were collected by Stanford University in 1989 as part of the U.S. Geological Survey Pacific to Arizona Crustal Experiment that traversed the Arizona Transition Zone of the Colorado Plateau. The results of independent waveform modeling methods are consistent with much of the lower crustal reflectivity resulting from thin, high-impedance layers. The reflection polarity of the cleanest lower crustal events is positive, which implies that these reflections result from high-velocity contrasts, and the waveform character indicates that the reflectors are probably layers less than or approximately equal to 200 m thick. The lower crustal events are generally less reflective to incident S waves than to P waves, which agrees with the predicted behavior of high-velocity mafic layering. Analysis of the P wave AVO character of lower crustal reflections demonstrates that the events maintain a constant amplitude with offset, which is most consistent with a mafic-layering model. One exception is a high-amplitude (10 dB above background) event near the base of lower crustal reflectivity which abruptly decreases in amplitude at increasing offsets. The event has a pronounced S wave response, which along with its negative AVO trend is a possible indication of the presence of fluids in the lower crust. The Arizona Transition Zone is an active but weakly extended province, which causes us to discard models of lower crustal layering resulting from shearing because of the high degree of strain required to create such layers. Instead, we favor horizontal basaltic intrusions as the primary origin of high-impedance reflectors based on (1) The fact that most xenoliths in eruptive basalts of the Transition Zone are of mafic igneous composition, (2) indications that a pulse of magmatic activity crossed the Transition Zone in the late Tertiary period, and (3) the high regional heat flow observed in the Transition Zone. The apparent presence of fluids near the base of the reflective zone may indicate a partially molten intrusion. We present a mechanism by which magma can be trapped and be induced to intrude horizontally at rheologic contrasts in extending crust.