Freight transportation is an integral element of various supply chains and has a complex and dynamical interrelationship with human economic activities. Modern logistical strategies paved way to the current supply chain organisation and logistics network design resulting in a more global economy and huge economies of scale. Recent trends of volatility of oil price have major implications in the movement of commodities across the supply chains. Likewise, climate change issues have presented urgent challenges in reducing carbon emissions for the transport and logistics sector. Pressure on the sector comes from both governments and consumers alike, demanding future sustainability as well as corporate environmental and social responsibility. The original contribution of this research is to investigate the system-wide dynamics of freight transportation and production in the context of supply chains. A theoretical framework called the ‘Geographic Adaptive Potential’ or GAP is built to understand how constraints in energy and emissions affect the production and distribution of commodities. The changes in the supply chain were investigated in four different components, namely a) the potential to shift to less energy and emissions intensive modes for long-haul freight, b) logistical strategies in the last leg of the chain or urban freight and c) local production and distribution, and d) the accessibility of potential customers to the markets. The design of the GAP components is in correspondence with the links of the supply chain. The analyses yielded an evaluation of the adaptive capacity of the freight transport and production system. For long-haul freight, a GIS-based model was created called the ‘New Zealand Intermodal Freight Network’ or NZIFN. It is an optimisation tool integrating the road, rail and shipping network of New Zealand and calculates that minimum time, operating costs, energy and emissions routes between 2 given locations. The case studies of Auckland to Wellington and Auckland to Christchurch distributions of non-perishable products established that even a marginal increase of rail and coastal shipping share produced around 10% reduction in both freight energy and greenhouse gas emissions. In the study of the last leg of the supply chain, the truck trip generation rates of different food stores were investigated. The strongest factors influencing the trip rates to a store are its size and product variation, the latter being a new parameter introduced in the dissertation. It is defined as the total number of brands for 6 chosen commodities commonly found in the stores. The trip rates together with the truck type and distance travelled were used to compute the freight energy usage of the stores. Results revealed that supermarkets consume the most energy for their delivery operations but relative to its physical size, they are more energy efficient than smaller stores. This is due to the utilisation of advanced logistical strategies such as freight consolidation and the effective use of distribution centres. The localised production chapter was explored in the context of Farmers’ markets and their difference with the conventional supermarket distribution system. Using a freight transport energy audit, the energy intensities of both systems were compared. The findings showed that Farmers’ markets were more energy-intensive than supermarkets owing to the low volumes of goods delivered to the market and the lack of freight consolidation effort in the system. The study on the active mode access of potential customers to both Farmers’ markets and supermarkets captured the interplay between freight and personal transport and is the final component of GAP. The results of the ArcGIS based model called ‘Active Mode Access’ or AMA demonstrated that both Farmers’ markets and supermarkets have the same level of accessibility for walking or biking customers. However, the calculations also showed that almost 87% of New Zealanders have no AMA to stores and are at risk for fuel price increase. Finally, the key result of this dissertation is the assessment that there is actually limited adaptive capacity of the freight transport and production system. This is due to network infrastructure and geographical constraints as well as commodity type and mode compatibility and other operational concerns. Due to these limitations, the GAP model assessed that reduction in energy and allowable emissions will ultimately reduce the amount of commodities moved in the system.