Understanding the diffusive transport behavior of volatile organic compounds (VOCs) in near-surface soils is important because soil VOC emissions affect atmospheric conditions and climate. Previous studies have suggested that temperature changes affect the transport behavior; however, the effect of these changes are poorly understood. Indeed, under dynamic temperature conditions, the change in VOC flux is much larger than that expected from the temperature dependency of the diffusion coefficient of VOCs in air. However, the mechanism is not well understood, although water in soil has been considered to play an important role. Here, we present the results of experiments for the upward vertical vapor-phase diffusive transport of two VOCs (benzene and tetrachloroethylene) in sandy soil under sinusoidal temperature variations of 20–30 °C, as well as its numerical representation. The results clarify that the unexpectedly large changes in emission flux can occur as a result of changes in the VOC concentration gradient due to VOC release (volatilization) from/trapping (dissolution) into water, and that such flux changes may occur in various environments. This study suggests the importance of a global evaluation of soil VOC emissions by continuous measurements in various soil environments and/or predictions through numerical simulations with thorough consideration of the role of water in dynamic soil environments.