Here we delve into the challenges and innovative strategies for achieving net-zero emissions in the wastewater sector, a notable source of global greenhouse gases. Unlike other infrastructure sectors, wastewater management involves complex and variably quantifiable emissions across all scopes, making standardization difficult. This study provides a global overview of the sector’s emissions profiles by leveraging literature mining, data analysis and case studies. It emphasizes the substantial variability in emissions, identifies key emission sources and locations, and advocates for tailored monitoring and mitigation strategies. It highlights the potential emissions shifting across scopes due to the adoption of new technologies and accounting practices, and it argues for a holistic analysis for optimization and integration to ensure a net benefit of the overall reductions in carbon footprints. This study underscores the urgency of rethinking current practices to align with ambitious mid-century net-zero targets, emphasizing the critical role of accurate emissions quantification and comprehensive decarbonization strategies.