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Small ponds account for a disproportionately high percentage of carbon dioxide emissions relative to their small surface area. It is therefore crucial to understand carbon flow in these ponds to refine the current global carbon budget, especially because climate change is affecting pond hydrology. High elevation ponds in the Elk Mountains of western Colorado are drying more frequently as the timing of snowmelt advances. We compared CO2 concentrations and fluxes among ponds of different hydroperiods over diel sampling periods during the course of the 2017 open-water period. CO2 concentrations were significantly negatively correlated with pond depth and averaged 77.6 ± 24.5 μmol L−1 (mean ± S.E.) across all ponds and sampling events. Ponds were up to twenty times supersaturated in CO2 with respect to the atmosphere. Flux was highly variable within individual ponds but correlated with time of sampling and was highest at night. Flux averaged 19.7 ± 18.8 mg CO2 m−2 h−1 across all ponds and sampling events. We also compared flux values obtained using modeled and empirical methods and found that widely-applied models of gas exchange rates using wind-based gas exchange (K) values yielded estimates of CO2 flux that were significantly higher than those obtained using the floating chamber approach, but estimates of CO2 flux using globally averaged convection-based K values were lower than those obtained using the floating chambers. Lastly, we integrated soil vs. water efflux measurements with long-term patterns in hydrology to predict how total season-long efflux might change under the more rapid drying regimes and longer seasons that are already occurring in these systems. Because soil CO2 efflux averaged 277.0 ± 49.0 mg CO2 m−2 h−1, temporary ponds emitted 674.1 ± 99.4 kg CO2 m−2 over the course of the 2017 season from ice-out to refreezing, which was over twice as much as permanent and semi-permanent ponds. Our results emphasize that contributions of CO2 from small ponds to the global carbon budget estimates will vary with pond hydroperiod and sampling methodology, which have been overlooked given that most previous estimates were collected from limited sampling periods and from pond waters alone. Furthermore, pond CO2 contributions are predicted to increase over time as pond areas transition from efflux from water to efflux from soil.