This study aims to investigate the effect of climate change on transportation flows and inland waterways in the Mississippi River Basin due to climate-induced shifts in crop production patterns in 2050 using two large scale modeling systems, an Agricultural Sector Model (ASM) and an International Grain Transportation Model (IGTM), with technical approach developed to link the two models. Simulated results from ASM show that 1) US and total social welfare rises; 2) crop producer welfare varies across US regions; 3) production and prices of all crops including corn and soybeans also varies; 4) National total cropland use increases with the expansion of irrigated land and contraction of dryland. After breaking down crop acreage results of ASM to the county level and reaggregating to the crop reporting district (CRD) level, which is the spatial scale employed in IGTM. Our study finds that overall supply of corn and soybeans likely increases in the Northern part, while it tends to decline in some areas from Central to Southern parts of the US. By subtracting demand for grains assumed to constant overtime with simulated supply of grains, we obtain the amount of excess supply and demand for grains, which are used as inputs in IGTM. Various interested findings from IGTM are revealed. For example, Corn Belt, the largest producer of corn in the US, is anticipated to ship less corn supply to Pacific, Northeast, Rocky Mountains, Southeast, and Mississippi Lower ports, while the Great Lakes ports, Lake States, and the Great Plains are expected to receive higher corn shipments from Corn Belt. For the aspect of export, the importance of Lower Mississippi ports, the largest destination for grain export from the US to the rest of the world, is going to diminish, where as the role of Pacific Northwest ports are simulated to increase. Considering overall demand for modes of transportation for total grain shipments, demand for rail and truck is expected to rise, while demand for barge mode is projected to drop.