In many parts of the world sedimentary horizons with potential for hydrocarbon are located below flood basalt provinces. However, the presence of high velocity basaltic overburden makes delineation of sediments difficult due to the low velocity layer problem. Electrical and electromagnetic methods have been used in such scenarios because of the good electrical conductivity contrast between basalts and underlying sediments. However, mapping of the target sediments becomes difficult when the layer is thin as the data errors due to inherent noise lead to equivalent solutions. To tackle such difficult situations, a joint inversion scheme incorporating seismic reflection and refraction, magnetotelluric and deep electrical resistivity datasets is presented. Efficacy of the scheme is tested for a model comprising a thin sedimentary layer sandwiched between a thick basalt cover and a granitic basement. The results indicate that the parameters of the target sedimentary layer are either poorly resolved or equivalent solutions are obtained by the inversion of individual datasets. Joint inversions of seismic reflection (RFLS) and refraction (RFRS), or DC and MT dataset pairs provide improved results and the range of equivalent solutions is narrowed down. Combination of any three of the above datasets leads to further narrowing of this range and improvements in mean model estimates. Joint inversion incorporating all the datasets is found to yield good estimates of the structure. Resolution analysis is carried out to appraise estimates of various model parameters obtained by jointly inverting different combinations of datasets.