This dissertation elucidates the value of H₂ and CO₂ infrastructure in decarbonising “difficult-to-abate” sectors of the economy. We analyse infrastructure for low-carbon fuels and energy vectors at different scales, and present a flexible formulation to integrate relevant technologies for their interconversion. We use a mixed integer linear programming (MILP) approach to formulate spatial systems optimisation problems, and identify solutions that can accelerate the transition to low-carbon systems. The modelling framework can incorporate spatial and temporal granularity, whilst also capturing the nuances of a site, country, or an industrial cluster. Through its application, we outline a transition pathway for the natural-gas based heating sector to H₂ in Great Britain, noting the key barriers to cost-effective deployment. The cost-optimal supply mix contains natural gas reforming with CCS, flexible electrolytic H₂ production, large volumes of salt cavern storage, and biomass gasification with CCS to offset any remaining methane and CO₂ emissions from the natural gas supply chain, and the production plants. Given the uncertainties involved, we note that a complete conversion of the gas grid in the UK to H₂ for heating buildings is unlikely to be viable. We find that a portfolio-based approach containing post-combustion CO₂ capture, fuel switching with H₂, and negative emissions is a cost-effective strategy to decarbonise industrial clusters in the UK. This achieves greater decarbonisation and avoids an overreliance on CO₂ emission offsets. The total costs of CO₂ avoidance can be reduced by using existing fuels such as refinery fuel gases for H₂ production. Natural gas plays an important role as fuel and feedstock for post-combustion and methane reforming, and is the primary determinant of the total costs of the system. This has implications for the security of supply, given that countries such as the UK import as much natural gas as they produce domestically. A cradle-to-gate lifecycle assessment of reforming, and electrolytic H₂ production using grid power and offshore wind power, shows that the lowest global warming potential is generated using a dedicated renewable-led supply. However, none of the production pathways are dominant across all key environmental performance indicators. This indicates the potential for “problem shifting” to occur by solely focussing on a given pathway for long-term supply development. We note that the environmental performance of H₂ improves with reductions in upstream methane emissions, and an increase in the capacity factor of renewable power generation assets.