Greenhouse gas (GHG) accounting protocols have addressed emissions from wastewater conveyance and treatment using a variety of simplifying methodologies. While these methodologies vary to some degree by protocol, within each protocol they provide consistent tools for organizational entities of varying size and scope to report and verify GHG emissions. Much of the science supporting these methodologies is either limited or the protocols have failed to keep abreast of developing GHG research. This state-of-the-art review summarizes the sources of direct GHG emissions (both those covered and not covered in current protocols) from wastewater handling; provides a review of the wastewater-related methodologies in a select group of popular protocols; and discusses where research has out-paced protocol methodologies and other areas where the supporting science is relatively weak and warrants further exploration.