Livestock are one of the largest single sources of methane emissions, which is a greenhouse gas. In this study, alfalfa meal was tested as a feed additive to lower the methane generation in the three species of waterfowl. Four experiments were conducted to determine methane generation in the intestines of Muscovy ducks, mule ducks and White Roman geese of the same age and with the same diet. In experiment I, the in vitro methane generation of the cecal contents was the largest compared to other intestinal compartments in each species (p < 0.05). Moreover, the methane generation of the cecal content or colon and rectum in goslings was higher than in mule and Muscovy ducklings (p < 0.05) at six weeks of age. In experiment II, the cumulative methane generation in the cecal content of mule ducks at 8 weeks of age was the largest among all species (p < 0.05). In experiment III, 4-month-old Muscovy ducks had the highest average methane generation per bird per day among the three species (p < 0.05). In experiment IV, the methane generation of the cecal content in birds fed a grower diet supplemented with a 30% alfalfa meal diet was lower than that of birds fed grower diet for all three species. Based on the above results, it is suggested that age, the method of measurement (in vitro vs. in vivo) and composition of diet significantly affect the level of methane generation in the intestine for Muscovy ducks, mule ducks and White Roman geese. The amounts of methane generation of the cecal contents in the three species were 36.1, 13.9, and 34.2 µg/g/4 h, respectively. By adding 30% alfalfa meal, the cumulative methane generation of the cecal contents for the three species were reduced by 63.3–95.5%. The addition of alfalfa meal to feed thus has good potential with regard to decreasing greenhouse gases emissions from waterfowl.