Process industries in New Zealand use 214.3 PJ of process heat, of which approximately 65 % is fossil fuels. Despite increasing energy demands, depleting fossil fuel resources, and pressure to reduce Greenhouse Gas emissions, low grade heat in large-scale processing sites is still not fully utilised. This thesis presents methods to target, optimise and design more practical heat recovery systems for large industrial sites, i.e. Total Sites, and overcome technical limitations of current methods. Original contributions of this thesis to literature include novel developments and applications in six areas: i) a new Total Site Heat Integration (TSHI) targeting method – Unified Total Site Targeting (UTST) – which sets realistic targets for isothermal and non-isothermal utilities and heat recovery via the utility system; ii) a new TSHI optimisation and utility temperature selection method to optimise Total Cost of the utility system; iii) a new Utility Exchanger Network synthesis and design method based on the targets achieved by the UTST method and optimal temperatures from optimisation method; iv) a new method for calculating assisted heat transfer and shaft work to further improve TSHI cogeneration and performance; v) examination of heat transfer enhancement techniques in TSHI to achieve higher heat recovery and lower required area by substituting conventional utility mediums by nanofluids in the utility system; and vi) a spreadsheet software tool called Unified Total Site Integration to apply the developed methods to real industrial cases. The developed methods have been applied to three large industrial case studies. Results confirm that heat recovery and utility targets obtained from the UTST method were lower but more realistic to achieve in practice when compared to conventional TSHI methods. The three industrial case studies represent a wide variety of processing industries. In summary, the over-estimation of TSHI targets for the three case studies from using the conventional method compared to the new method are 0.2 % for the Södra Cell Värö Kraft Pulp Mill, 22 % for a New Zealand Dairy Factory, and 0.1 % for Petrochemical Complex. The Total Annualised Costs (TAC) for the three case studies are minimised using a new derivative based approach. Results show TAC reductions 4.6 % for Kraft Pulp Mill, 0.6 % for Dairy Factory, and 3.4 % for Petrochemical Complex case studies. In addition, sensitivity analysis for the optimisation is undertaken. The UTST method with its modified targeting procedure is demonstrated to generate simpler Utility Exchanger Network designs compared to conventional methods, which confirm the original targets are realistic and achievable. A new method for calculating assisted heat integration targets applied to an example Total Site problem increased heat recovery by 1,737 kW, which is a 21% increase in Total Site heat recovery, and increased shaft work by 80 kW. Lastly, the addition of nanoparticles to create a closed nanofluid heat recovery systems shows heat recovery from liquid-liquid heat exchangers increases of 5 % to 9 % using an intermediate fluid with 1.5 vol. % CuO/water.