Small and shallow water bodies often exhibit high rates of biogeochemical activities, yet have not received much attention. Here we test the hypothesis that there is strong diurnal stratification of physicochemical characteristics in a hyper-eutrophic pond, which would lead to a heterogeneous distribution of gas production via biological processes along vertical profile of water column. Accordingly, we focused on quantifying the seasonal and diurnal dynamics of nutrients (NO3−, , total dissolved nitrogen TDN, PO43−, total dissolved phosphorus TDP), physicochemical environment factors (DO, pH, light intensity, Chlorophyll-a) and gas emission (N2, N2O, O2, CH4) in the vertical profile of an ultra-eutrophic pond located at the subtropical climate zone, China. The strong and persistent stratification of several parameters at the resolution of centimeters along vertical profile of water was observed in summer and autumn. Interestingly, the surface water and sediment–water interface produced much more gas than the middle layers of water column. The quantity and composition of gas collected from the surface water were greatly affected by O2 production, which followed the diurnal cycle of sunlight intensity. Other biological processes, e.g. nitrification and/or denitrification, may also have contributed to the heterogeneous gas production as high N2 and N2O fluxes were detected in the surface layer and sediment–water interface. CH4 production was mainly from the sediment–water interface, especially in summer when the bottom layer developed very low DO concentrations due to strong stratification. Our results demonstrate that besides the unexpectedly long and strong thermal and physicochemical stratification, the shallow eutrophic pond can undergo significant vertical heterogeneity of gas emission due to the strong diurnal stratification of these physicochemical parameters.