River systems are expected to have a great potential to transport cargoes especially under disaster conditions. In Hanshin Earthquake disaster occurred in 1995, ship transport of relief goods by rivers worked effectively. Furthermore the alternative routes other than transportation on land under disaster circumstances are required strongly. The ship transport of relief goods by rivers meets with this requirement. This paper describes a way to estimate the capacity of ship transportation by rivers with multi-agent simulation. Simulation results clarify the structure of bottlenecks that restrict the amount of transportation under disaster circumstances described in this paper. Firstly the supplying capacity, such as loading speed to vessels, is most important factor. Secondary the receiving capacity at a birth of suffering areas becomes important. If the capacity of both receiving and supplying is sufficient, the number of ships results in shortness.