AbstractNowadays, with population growth, rising global energy demand, increasing water consumption, carbon emissions, and excessive use of fossil fuels, the world faces a major challenge. Biomass is one of the most attractive sources of energy production, with positive effects on the economy, environment, and society, which can decrease the world's reliance on fossil fuels and deal with this universal challenge. Consequently, the biomass supply chain network design has received more attention in recent decades. Since energy and water are two significant sources for society's sustainable development and carbon emissions are essential for environmental health, the study of the water–energy–carbon (WEC) nexus is essential. In this study, a multiobjective multiperiod model for designing a sustainable supply chain network based on hybrid second‐generation (i.e., Jatropha, agricultural waste, and animal waste) and third‐generation (i.e., microalgae) biomasses is presented. The proposed multiobjective model consists of five objective functions that maximize the total energy produced and the number of jobs created and minimize the total water consumed, carbon emitted, and total costs. Case study results demonstrate the performance of the model utilizing the MINMAX goal programming approach. Based on the results, energy production from Jatropha is more appropriate in comparison with energy production from microalgae, agriculture waste, and animal waste. The findings also show that the proposed model in this research considering the WEC nexus performs significantly better than the classical model without considering the WEC nexus.