[This dataset is embargoed until May 31, 2024]. These data include greenhouse gas concentrations and physio-chemical water properties for the Clyde estuary in Scotland to support understanding of the GHG sources and sinks and their associated mechanisms in a highly stratified, temperate urban estuary. These measurements look at the changes in GHG along the Clyde estuary taking measurements from land to sea down the estuary on the ebb tide at both the surface and bed so the impact of location, river flow, wastewater treatment outflows and stratifications can be understood. Full details about this dataset can be found at https://doi.org/10.5285/a22b495e-b2cd-43cd-95b7-8712b64dc0da