Mangrove forests help regulate Earth’s climate by storing carbon dioxide, but they can also release other powerful greenhouse gases like methane and nitrous oxide. In this study, we measured greenhouse gas emissions at eight mangrove sites across the city of Shenzhen, China. We looked at both gas release from sediments and dissolved gas levels in nearby surface water. We found that many sites, especially those in more developed areas, released higher levels of methane and nitrous oxide than less disturbed sites. The surface waters were also oversaturated with these gases compared to what would be expected from air–water balance, showing that the water itself is an important source of emissions to the atmosphere. By analyzing the chemical fingerprints (isotopes) of these gases, we were also able to trace their microbial sources. This study provides new insights into greenhouse gas emissions from urban mangroves and highlights how these emissions can vary across different locations within the same city.