The understanding of depositional setting, the aquifer properties and the groundwater flow within an intermontane basinis of great significance for groundwater abstraction and monitoring. Among different intermontane basins developed in northwestern Himalaya, Pakistan, the Bannu Basin is very important and is filled with Quaternary sediments. The electrical resistivity data was acquired, processed and interpreted in two separate plains of the Bannu Basin, i.e. the Lakki Marwat Plain and the Domail Plain. The Domail Plain lies in the eastern section of the Bannu Basin whereas the Lakki Marwat Plain is located in the western half. Through a combination of geostatistical analysis, geophysical inversion and visualization techniques it is possible to re-model and visualizes the single dimension resistivity data into 2D and 3D spaces. Variogram models are utilized to extend the interpretation of the data and to distinguish individual lithological units, as well as the occurrence of saline water within the subsurface. As such the alluvial system of the intermontane basin has formed during episodes of local tectonic activity with fluvial erosion and deposition yielding coarse sediments with characteristically high electrical resistivities near to the mountain ranges and finer sediments of medium to low electrical resistivities towards the basin center. The regional and local tectonic activity has caused a considerable amount of faulting in the rocks as well as depressions which over time, have been filled with clay-silt sediments typical of lacustrine and flood plain environments. Streams arising in the adjacent mountains have eroded these sediments leaving gravel–sand deposits in channels. It is concluded that these sediments have been deposited in several different depositional settings including prograding fan shaped bodies, flood plains, sandy plain and lacustrine deposits. The depositional setting of the sediments influences the groundwater flow movements within the plains. The work was further extended to estimate the aquifer properties utilizing vertical electrical sounding (VES) and pumping test data sets acquired in the Lakki Marwat and Domail Plains of Bannu basin. The sediments in the alluvial fan zones are characterized by low gamma ray values which suggest low levels of fine sediments. This is in contrast to the sandy plain and lacustrine zones where higher gamma ray values suggest higher contents of the finer material. The alluvial fan zones have the maximum transmissivity in the area, while the sandy plain and lacustrine zones exhibit very low transmissivities. This indicates a higher concentration of finer material within the sandy plain and lacustrine zones with the absence of the recharge boundaries, thus reducing the effective water transmission. The steady state groundwater flow pattern roughly follows the resistivity patterns within the aquifer system and generally flow towards the Gambila River within the Lakki Marwat Plain. The water flow is regular and uniform within the higher resistivity zones, whereas the flow patterns in the lower resistivity zone representing the lacustrine environment is generally retarded. The water table has a steady rise in the lacustrine zone due to the less transmission of water in the lacustrine zone. The correlation between resistivity zones and the groundwater flow in Domail Plain is difficult to establish, because a considerable portion of the subsurface has been masked by saline water. In this plain groundwater flows steadily towards the Kurram River roughly follow the topography of the plain. The regional trends in the depositional systems in conjunction with the groundwater flow patterns identify the prospective groundwater development zones within the subsurface. The prospective zones identified within the basin when evaluated further would help in management of the important groundwater resource within the region. The regional scale interpretation of seismic, well logs and electrical resistivity data sets highlight the tectonic activity in the region resulted in the formation of northwestern Himalayan fold and thrust belt and the associated intermontane basins.