Small ponds comprise a substantial portion of the total area of the Earth’s inland waters. They can be powerful carbon sinks or sources, potentially significant processors of organic carbon. Our understanding of their role is constrained by the absence of information regarding their CO2 fluxes (F CO2) and how these change with wet or dry phases and across distinct pond plant communities. We monitored the F CO2 from 26 neighbouring small ponds over a two week drying period in late summer in 2014. The mean F CO2 on day 1 (-641 ± 1490 mg m-2 d-1) represented a net intake across the site. As ponds dried they switched to becoming CO2 sources resulting in a net site emission of CO2 by day 12 (3792 ± 2755 mg m-2 d-1) although flux rates did not vary systematically between plant communities. Significant variability in the F CO2 was observed among adjacent ponds on individual sampling days, resulting in marked spatial heterogeneity in CO2 processing. This large degree of temporal and spatial heterogeneity across short time periods and small distances highlights the variability in the F CO2 from temporary systems, making it hard to generalize their role in carbon cycle models.