Environmental concerns about the effect of greenhouse gases have led governments to regulate industrial CO2 emissions, including through emissions caps, trading and penalties, thus creating economic incentives to reduce CO2 emissions. This research focuses on strategies to reduce CO2 emissions from energy systems in the context of the process industries. In the process industries, energy systems consume fuel to generate steam and power for site process units. Improving energy efficiency can reduce costs of energy generation and use, as well as CO2 emissions. This research develops an integrated design and optimisation methodology for energy systems, allowing effective capture and control of carbon dioxide emissions. The first focus of this study is to develop a systematic approach to evaluate combinatorial strategies for reducing CO2 emissions, based on a techno-economic analysis. A conceptual design procedure with hierarchical decision-making is introduced to combine CO2 emissions reduction strategies, accounting for interactions between site components, including the heat exchanger network and utility system. CO2 emissions reduction options considered in development of this procedure include process integration techniques for improving the energy efficiency of the site and fuel switching. The proposed approach considers trade-offs between the economy of energy retrofit and CO2 emissions penalties. Opportunity for reducing the CO2 penalty is included in the economic evaluation of the combined emissions reduction strategies. A mathematical model for simultaneous optimization of emissions reduction strategies is developed. In addition to emissions reduction strategies, options for trading CO2 allowances are considered in the model. The proposed mathematical method applies Mixed Integer Non Linear Programming (MINLP) optimization, which employs a superstructure of the strategies for CO2 reduction. The proposed mathematical model relates the selected options to their operating and capital costs and to their associated CO2 emissions, allowing the optimizer to search for the optimal combination of emissions reduction strategies. While the reduction in CO2 emissions through process integration techniques is based on the existing configuration of a site and the associated structural limitations, integration of Carbon Capture and Storage (CCS) technologies can provide greater mitigation of CO2 emissions from a site. However, important challenges of implementing CCS in the process industries are the energetic and economic impact of the CCS plant on the integrated site. In the second part of this study, these energy-economic issues are explored. The CCS technologies addressed in this thesis include post- and pre-combustion CO2 capture techniques. Simulation of each capture technique is carried out in process simulation software to characterize the energy performance of the CO2 capture plant. Sensitivity analyses are carried out for key parameters of the CO2 capture plant. The relationship between these key parameters and the energy balance of the capture plant is represented using a simple energy performance model for the CO2 capture plant. This model allows the integration of the CO2 capture plant with the site utility system to be explored. Interactions between the utility system and CO2 capture plant are considered. The site utility system, together with the CO2 capture plant, is optimized for minimum operating cost. The proposed procedures are illustrated by application to a case study of a medium-scale oil refinery. The results illustrate that to reduce CO2 emissions, heat integration, utility system optimization and fuel switching provide more cost-effective solutions than integrating CCS technologies. The mathematical model allows more cost-effective solutions to be identified than using sequential, conceptual methods, but the value of the conceptual method for developing insights is also illustrated. The results demonstrate that, depending on the potential of the site for increasing heat recovery and the type of fuel used on site, solutions that combine energy efficiency and fuel switching can provide up to 40% reduction in site CO2 emissions. Integrating a post-combustion CO2 capture plant with the site utility system can provide up to 90 mol% pure CO2 for sequestration; however, the high capital cost of the capture plant reduces the economic performance of the integrated site. The high heat demand of post-combustion CO2 capture for solvent regeneration increases the fuel consumption of the site and its utility system, which in turn reduces the recovery of CO2. The results reveal that pre-combustion CO2 capture can provide opportunities for heat and power generation to improve the techno-economic performance of the overall integrated site.