Nano- and microparticle tracers are expected to be used for evaluating structures in geological developments, however their transport behavior is not well characterized. This study investigated nanoparticle transport in a fractured medium through a microscope. A single fracture and rock matrix (grain and pore space) were fabricated on a silicon wafer, which is called a micromodel. Water and nanoparticles were injected into the micromodel, and the temporal change of particle concentration was measured by analyzing the scanning electronic mirror (SEM) images of the dried droplet. The response curve showed a peak at early time followed by a long tail, which suggests that some particles flowed through the fracture in the micromodel and others migrated through the matrix space. Tunable Resistive Pulse Sensing (TRPS) was also used to obtain temporal changes of the particle concentration. The larger particles were observed only at early time, while the smaller particles were detected over a wider range of time. This indicates that particles with different sizes transport through fractured media differently depending on the fracture structures and that the tracer response may be useful to evaluate the flow properties for each flow path.