Despite the great advance brought by the National Interconnected System (NIS), which is able to provide clean hydroelectric power to almost all Brazilian customers, there are still cities supplied by power generated from fossil fuel, which are subsidized by taxes, they are called Isolated Electric Power Systems (IEPS). Pará State, that has 34 cities with IEPS, also has potential to crop raw material (palm and sugar cane) to produce biodiesel for power generation. Our study analyzes the supply and distribution network of biodiesel under some scenarios of waterways availability, considering that they are also source of power to the NIS by the construction of hydroelectric dams. We develop specific demand and facility location models and apply them to the scenarios. Our results point to the efficiency of the generated models, the importance of three cities for the network, and to the little impact of some waterways in the total transportation costs.