Nowadays required energy mostly comes from fossil fuels but the limitation of fossil resources and their environmental effects have encouraged communities to seek alternative renewable energy sources. Meanwhile enery forom biomass (bioenergy) has particular importance due to wide range of resources and other advantages. In this research, a multi-objective model is proposed to design a bioenergy supply network from different types of second-generation biomass (Jatropha, agricultural residue and animal waste) and third generation (microalgae) considering water-energy nexus and carbon emission concepts. Geographic Information System (GIS) is used in order to find proper places for Jatropha cultivation in Iran and reduce the solution space. The proposed model is solved for a 10 years time horizon using MINMAX goal programming method for Iran provinces as a case study. According to the results, energy production from microalgae and Jatropha resources is prior to the waste.