Fluvio-deltaic aquifers are the primary source of drinking water for the people of Bangladesh. Such aquifers, which comprise the Ganges-Brahmaputra-Meghna Delta, are hydrogeologically heterogeneous. Because of widespread groundwater quality issues in Bangladesh, it is crucial to know the hydrostratigraphic architecture and hydrochemistry, as some aquifer units are contaminated, whereas others are safe. Geophysical methods provide a potentially effective and noninvasive method for extensive characterization of these aquifers. This study applies and investigates the limitations of using electrical resistivity imaging (ERI) for mapping the hydrostratigraphy and salinity of an aquifer-aquitard system adjacent to the Meghna River. Some electrical resistivity (ER) sections showed excellent correlation between resistivity and grain size. These suggest that ERI is a powerful tool for mapping internal aquifer architecture and their boundaries with finer-grained aquitards which clearly appear as low-ER zones. However, in parts of some ER sections, variations in electrical properties were determined by porewater resistivity. In these cases, low ER was indicative of brine and did not indicate the presence of finer-grained materials such as silt or clay. Accordingly, the following hydrostratigraphic zones with different resistivities were detected: (1) aquifers saturated with fresh groundwater, (2) a regional silt/clay aquitard, and (3) a deeper brine-saturated formation. In addition, shallow silt/clay pockets were detected close to the river and below the vadose zone. ERI is thus a promising technique for mapping aquifers versus aquitards; however, the observations are easily confounded by porewater salinity. In such cases, borehole information and groundwater salinity measurements are necessary for ground-truthing.