Greenhouse gas emissions are likely to rise faster than growth in population and more than double for water supply and wastewater services over the next 50 years in South East Queensland (SEQ), Australia. New sources of water supply such as rainwater tanks, recycled water, and desalination currently have greater energy intensity than traditional sources. In addition, direct greenhouse gas emissions from reservoirs and wastewater treatment and handling have potentially the same magnitude as emissions from the use of energy. Centralized and decentralized water supply and wastewater systems are considered for a scenario based upon a government water supply strategy for the next 50 years. Many sources of data have large uncertainties which are estimated following the IPCC Good Practice Guidelines. Important sources of emissions with large uncertainties such as rainwater tanks and direct emissions were identified for further research and potential mitigation of greenhouse gas emissions.