This dissertation studies two important problems in the field of biomass supply chain network. In the first part of the dissertation, we study the impact of different carbon regulatory policies such as carbon cap, carbon tax, carbon cap-and-trade and carbon offsetmechanism on the design and management of a biofuel supply chain network under both deterministic and stochastic settings. These mathematical models identify locations and production capacities for biocrude production plants by exploring the trade-offs that exist between transportations costs, facility investment costs and emissions. The model is solved using a modified L-shaped algorithm. We used the state of Mississippi as a testing ground for our model. A number of observations are made about the impact of each policy on the biofuel supply chain network. In the second part of the dissertation, we study the impact of intermodal hub disruption on a biofuel supply chain network. We present mathematical model that designs multimodal transportation network for a biofuel supply chain system, where intermodal hubs are subject to site-dependent probabilistic disruptions. The disruption probabilities of intermodal hubs are estimated by using a probabilistic model which is developed using real world data. We further extend this model to develop a mixed integer nonlinear program that allocates intermodal hub dynamically to cope with biomass supply fluctuations and to hedge against natural disasters. We developed a rolling horizon based Benders decomposition algorithm to solve this challenging NP-hard problem. Numerical experiments show that this proposed algorithm can solve large scale problem instances to a near optimal solution in a reasonable time. We applied the models to a case study using data from the southeast region of U.S. Finally, a number of managerial insights are drawn into the impact of intermodal-related risk on the supply chain performance.