As population and water demand increase, there is a growing need for alternative water supplies from water reuse and desalination systems. These systems are beneficial to water augmentation; however, there are concerns related to their carbon footprint. This study compiles the reported carbon footprint of these systems from existing literature, recognizes general trends of carbon footprint of water reuse and desalination, and identifies challenges associated with comparing the carbon footprint. Furthermore, limitations, challenges, knowledge gaps, and recommendations associated with carbon footprint estimation tools are presented. Reverse osmosis (RO) technologies were found to have lower CO2 emissions than thermal desalination technologies and the estimated carbon footprint of seawater RO desalination (0.4–6.7 kg CO2eq/m3) is generally larger than brackish water RO desalination (0.4–2.5 kg CO2eq/m3) and water reuse systems (0.1–2.4 kg CO2eq/m3). The large range of reported values is due to variability in location, technologies, life cycle stages, parameters considered, and estimation tools, which were identified as major challenges to making accurate comparisons. Carbon footprint estimation tools could be improved by separating emissions by unit process, direct and indirect emissions, and considering the offset potential of various resource recovery strategies.