Small waterbodies like floodplain ponds are considered to be an important component of the global carbon budget. Although they are found in large numbers worldwide and their numbers are increasing every year due to the creation of new ponds, we do not have sufficient data on direct estimates of emission fluxes from these waterbodies yet. Herein, we present results from a set of 24 ponds located in the Morava River floodplain, Czech Republic. The ponds varied in their origin (man-made vs. natural), size, depth, sediment organic matter content, and macrophyte growth. Water chemistry parameters, concentrations, and exchange of CO2 and CH4 with the atmosphere were directly measured during the day and night from spring to summer 2020. The ponds emitted more CO2 and CH4 during nighttime, and both CO2 and, in particular, CH4 emissions tend to increase with the duration of pond inundation. Total diffusive fluxes of CO2 and CH4 into the atmosphere ranged from −37072.9 to 432683.3 μmol m−2 d−1, and −11485.3 to 95,889.6 μmol m−2 day−1, respectively. Generally, all ponds were found to be a net source of CO2 and CH4 to the atmosphere. In average, ponds emitted 7.64 g CO2-equivalent m−2 d−1. Thus, our results indicate that floodplain ponds are an important source of both CO2 and CH4 to the atmosphere and they should not be omitted in a regional carbon budget.