The magnetotelluric (MT) method has been applied to the determination of the deep resistivity structure of the northeastern margin of the Parnaiba Basin. Transient electromagnetic (TEM) and MT data were collected in early 1999 along a 95 km long N–S line, extending from the coast across the projected subcrop position of a discontinuous fault found to the west of the study area that is believed to be a possible basin-bounding fault. The MT data were processed to yield the TE- and TM-mode responses and then corrected for static shift using central-loop and single-loop TEM data, respectively. Regularized 2D MT inversion was subsequently undertaken using a structured initial model with the near-surface constrained by TEM inversion results. As a consistency check, we performed another set of 2D inversions using different smooth initial models. The various optimal 2D inversion models show clearly the presence of a major basement trough, over 2 km deep, located about 70 km from the coast. We interpret it as possibly marking the main basin margin and suggest that it may have implications for groundwater resource development in the area.