We used Magnetotelluric (MT) and Electrical Resistivity Tomography (ERT) to investigate the geometry and nature of faults activity of the Okavango Rift Zone (ORZ) in Botswana, an incipient rift at the southern tip of the Southwestern Branch of the East African Rift System. The ORZ forms a subtle topographic depression filled with Quaternary lacustrine and fluvio-deltaic sediments and is bounded by NE-trending normal faults that are more prominent in the southeastern portion of the rift basin. An MT model from a regional (~140 km) NW-SE trending MT transect shows that much of the rift basin is underlain by a broad asymmetrical low resistivity anomaly that slopes gently (~1⁰) from NW to SE reaching a depth of ~300 m. This anomaly suggests that faults in the southeastern part of the rift form a NW-dipping border fault zone and that the lacustrine and fluvio-deltaic sediments contain brackish to saline water filling the broad half-graben structure. Furthermore, MT and ERT models from detailed (4-13 km long) MT transects and resistivity profiles show that one border fault (Thamalakane) and two within-basin faults (Lecha and Tsau) in the southeastern part of the ORZ are characterized by a localized high conductivity anomaly while another border fault (Kunyere) lacks such an anomaly. These localized anomalies are attributed to channelized fresh surface water and saline groundwater percolating through these faults forming "fault zone conductors" and suggest actively displacing faults. The lack of a "fault zone conductor" in the Kunyere fault is interpreted as indicating diminishing displacement on this fault, and that strain was transferred to the Thamalakane fault further to the east. The fluids provide lubricant for the ORZ faults, hence preventing infrequent large magnitude earthquakes, but favoring frequent micro-seismicity.