This work integrates perennial feedstock yield modeling using climate model data from current and future climate scenarios, land use datasets, transportation network data sets, Geographic Information Systems (GIS) tools, and Mixed integer linear programming (MILP) optimization models to examine biorefinery network designs in the southeastern United States from an overall systems perspective. Both deterministic and stochastic cases are modeled. Findings indicate that the high transportation costs incurred by biorefinery networks resulting from the need to transport harvested biomass from harvest location to processing facilities can be mitigated by performing initial processing steps in small scale mobile units at the cost of increased unit production costs associated with operating at smaller scales. Indeed, it can be financially advantageous to move the processing units instead of the harvested biomass, particularly when considering a 10-year planning period (typical switchgrass stand life). In this case, the mobile processing supply chain configuration provides added flexibility to respond to year-to-year variation in the geographic distribution of switchgrass yields. In order to capture the effects of variation in switchgrass yields and incorporate it in optimization models, yield modeling was conducted for both current and future climate scenarios. (In general profits are lower in future climate scenarios). Thus, both the effects of annual variation in weather patterns and varying climate scenarios on optimization model decisions can be observed.