An H-channel microfluidic device system was built to simulate the dead-end structures in subsurface environments. The accessibility to these restriction regions where significant amount of oil and contaminants may be trapped is challenging. Hence, large amount of unnecessary chemicals might be required for remediation and enhanced oil recovery (EOR) applications, making the process expensive and environmentally unfavorable. In this work, we demonstrate the ability of salinity gradients that naturally exist in the subsurface environment to target-migrate nano-capsules in porous and fractured rock formations. Our results demonstrate the concept and provide evidence of the potential of utilizing existing chemical and thermal gradients to enable autonomous and sustainable migration of nano-capsules into constricted regions in the subsurface environment for more efficient and environmentally-friendly subsurface remediation and energy harvesting applications.