Abstract. The self-sufficiency ratio of rice in Tokyo was less than 5 % but the national self-sufficiency ratio in Japan has reached over 90 % in 2012. Accordingly, local rice distribution is a key factor for regional food security but also water resource management because a significant amount of irrigation water was simultaneously used or saved in the production or consumption areas, respectively, through rice distribution. This study's aim is to analyze domestic rice distribution, and assess the dependency of prefectures on water resources within or outside the region through virtual water flows that indicate the embedded water in food trade. The results show that significant amounts of water were transferred virtually from the Northern regions such as Tohoku and Hokkaido to industrial and urbanized regions including Tokyo and Osaka through domestic rice distribution. In particular, the outflow of virtual water from the Tohoku region was more than 3 billion m³/yr during 2000–2012, and it was almost three times larger than the net flows of virtual water within the Tohoku region. In addition, increasing self-supply in the main producing prefectures affected the changes in the entire rice distribution network. In particular, as the self-supply in Shiga — the main producing prefecture sharing the Yodo-river basin with Osaka in the Kansai region — increases, the dependency of Osaka on virtual water flows from outside the Kansai region rises. Thus, it is important to consider the link between food and water through virtual water flow in trans-boundary water management, integrating not only water resource boundaries such as river basins, but also food boundaries covering production and consumption areas.