This study investigated the impact of optimum dosages of nano-calcium carbonate (nano-CaCO3) and nanosilica on the engineering behavior of black cotton soil. The desired percentage of nano-addition, 2%, for both nanomaterials, was determined by analyzing the plasticity-compaction characteristics and the relative strength index values of treated samples. The study unveiled that the entire clay microstructure was transformed into a nanocrystalline matrix after treatment. The deviatoric strength enhancement with confining pressure and curing period was significant after treating the soil with either nano-CaCO3 or nanosilica. The nanosilica treatment was found to be more effective in improving the California bearing ratio (CBR) strength of black cotton soil samples compared with nano-CaCO3 stabilization. The addition of nanomaterials induced the formation of nanocrystalline hydrate gels and silica gel, resulting in an increased resistance to volumetric deformation under compressive stresses. The hydraulic conductivity of nano-treated samples dropped due to the highly tortuous networks between pores in the nano-crystalline structure. The experimental results were substantiated by analyzing the microstructure of nano-treated soils using X-ray diffraction (XRD), scanning electron microscopy (SEM), and Fourier transform infrared (FTIR) techniques.