Indira Gandhi Canal Project has enhanced considerable food production in the desert area of Rajasthan, it also brought problems such as waterlogging and secondary salinisation. Impounding of Ghaggar flood water in natural depression is the main cause of seepage. Villages are located at a lower altitude than the level of water stored in depressions, which creates a steep gradient and sand dunes being pervious, causing heavy seepage. The steady rise of the water table causes waterlogging conditions in surrounding areas. The unlined canals from the saddle dams and continuous application of surface irrigation at higher frequencies have further added to the problem. One of the significant advantages of SAR is penetration through dry soil and detecting subsurface geological and fluvial features. This paper presents the results of identifying subsurface canal seepage in the sand dune area of Hanumangarh district, Rajasthan using multi-date MRS RISAT-1 SAR data. Signatures of high subsurface soil moisture accumulated in the depressions below the sand dunes and along the canal was analysed and identified as seepage areas. Landsat-8 images and field soil moisture data were used as complementary information to find the surface and subsurface soil moisture, crop and vegetation condition of the area. Subsurface moisture was identified with higher sensitivity in the cross polarizations (HV) images due to high volume scattering caused by the buried moisture-bearing structures. The cross-polarization ratio (CPR) observed was higher in the case of subsurface soil moisture than surface moisture signature. Significant depletion in soil moisture of seepage areas was observed in the images acquired during the month of June 2015.