Abstract. Shallow ponds can exist in a clear-water state dominated by macrophytes or a turbid-water state dominated by phytoplankton, but it is unclear if these two states affect differently carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) emissions to the atmosphere. Two clear-water urban ponds (Silex and Tenreuken) dominated by macrophytes, and two turbid-water urban ponds (Leybeek and Pêcheries) dominated by phytoplankton, in the city of Brussels (Belgium), were sampled 46 times between June 2021 and December 2023 to measure the partial pressure of CO2 (pCO2), dissolved CH4 concentration, N2O saturation level (%N2O), and ancillary variables. CH4 ebullitive fluxes were also measured in the four ponds during 8 deployments, totally 48 days of cumulated measurements. The 13C/12C ratio of CH4 (δ13C-CH4) was measured in bubbles from the sediment and in water to decipher the pathway of sedimentary methanogenesis (acetoclastic or hydrogenotrophic) and quantify methane oxidation (MOX) in the water column. The pCO2 and CH4 values in the sampled urban ponds correlated with precipitation and water temperature, respectively. The %N2O values did not correlate with dissolved inorganic nitrogen (DIN) nor other variables for the individual ponds, but a positive relation to DIN emerged from the combined data-set for the four ponds. The sampled turbid-water and clear-water ponds did not show differences in terms of diffuse emissions of CO2 and N2O. Clear-water ponds exhibited higher values of annual ebullitive CH4 fluxes compared to turbid-water ponds, most probably in relation to the delivery to sediments of organic matter from macrophytes. At seasonal scale, CH4 fluxes between the surface of the ponds and the atmosphere exhibited a temperature dependence in all four ponds, with ebullitive CH4 fluxes having a stronger dependence to temperature than diffusive CH4 fluxes. The temperature sensitivity of ebullitive CH4 fluxes was different among the four ponds and decreased with increasing water depth. During summer 2023, hydrogenotrophic methanogenesis pathway seemed to dominate in clear-water ponds and acetoclastic methanogenesis pathway seemed to dominate in turbid-water ponds, as indicated by the δ13C-CH4 values of bubbles sampled by physically perturbing sediments. The δ13C-CH4 values of bubbles sampled during bubble trap deployments in 2021–2023 indicated a seasonal shift to hydrogenotrophic methanogenesis pathway in fall compared to spring and summer, when acetoclastic methanogenesis pathway seemed to dominate. The δ13C-CH4 of dissolved CH4 indicated higher rates of MOX in turbid-water ponds compared to clear-water ponds, with an overall positive correlation with total suspended matter (TSM) and Chlorophyll-a (Chl-a) concentrations. The presence of suspended particles putatively enhanced MOX by reducing light inhibition of MOX and/or by serving as substrate for fixed methanotrophic bacteria in the water column. Total CH4 emissions in CO2 equivalents either equalized or exceeded those of CO2 in most ponds, while N2O emissions were negligible compared to the other two greenhouse gases (GHGs). Total annual GHG emissions in CO2 equivalents from all four ponds increased from 2022 to 2023 due to higher CO2 diffusive fluxes, likely driven by higher annual precipitation in 2023 compared to 2022, possibly in response to the intense El Niño event of 2023.