Whereas wetland ecosystems are among the most vital natural carbon sinks, they are also important sources of nitrous oxide (N2O), a highly potent greenhouse gas. However, due to differences in wetland characteristics, N2O emission is likely to vary across wetland types. We investigated the: 1) influence of vegetation community (Typha latifolia; Typha, Phragmites mauritianus; Phragmites and Cyperus papyrus; Papyrus) in a natural tropical freshwater wetland, and 2) impact of converting a natural tropical freshwater wetland into a rice paddy wetland on N2O emission. Results showed that N2O emission (µg m− 2 h− 1) from the natural wetland did not vary significantly (p > 0.05) among the vegetation communities during both the dry and wet seasons (Typha = 0.6 ± 1.6 [SE] and 0.5 ± 1.4, Phragmites = 0.5 ± 1.7 and 0.4 ± 1.5, Papyrus = 0.5 ± 1.3 and 0.5 ± 1.5, respectively). These emission rates insignificantly differed (p > 0.05) from those recorded in the rice paddy wetland (dry season = 0.7 ± 2.8 and wet season = 0.6 ± 2.7). There was no significant correlation (p > 0.05) between soil physico-chemical characteristics and N2O emission. We concluded that vegetation community does not affect N2O emission from a natural tropical freshwater wetland under continuous flooding. Similarly, under continuous flooding and no fertilization conditions, converting a natural tropical freshwater wetland into a rice paddy wetland does not influence N2O emission. We roughly estimated total annual N2O emissions (T yr− 1) and their carbon dioxide equivalents (CO2e; T yr− 1) from all Uganda’s natural and rice paddy wetlands as: natural wetlands = 115.1 ± 342.8 (CO2e = 30,501.5 ± 90,842) and rice paddy wetlands = 0.9 ± 2.7 (CO2e = 242.5 ± 707.6).