Methane emissions from flooded rice paddies are important contributors to the increasing atmospheric concentrations of methane, a potent greenhouse gas. With an increased need for rice agriculture to feed the growing global population, there is a need to develop methods that reduce methane emissions from rice paddies without adversely affecting grain yield. Two potential mitigation strategies were examined in this study: water management and cultivar choice. Previous studies indicate that floodwater management is a promising mitigation tool, with mid-season field drainage significantly reducing methane emissions. A variety of soil parameters, methane emissions, and soil porewater acetate concentrations were measured in outdoor pot and field water management studies. Acetate received particular consideration as it is a major precursor of methane formation within anaerobic soils. Field drainage caused rapid oxidation of the soil, with a sharp reduction in soil acetate concentrations, methane production, and methane emission rates. Evidence of drainage induced substrate depletion is presented as a possible mechanism responsible for the reduced methane production and emission after field drainage. Intervarietal differences in methane emission rates from rice have also been reported in previous studies. Methane emission rates and soil acetate concentrations were compared for a high emitting and a low emitting cultivar of rice. Significantly more soil acetate was present in the high emitting cultivar than the low emitting cultivar during the vegetative stage of plant growth. These results suggest that differences in methane emission between varieties of rice are the result of different methane production rates, not differences in methane transport processes. The different production rates are the result of differences in root carbon loss between the two cultivars. Neither of these strategies had an adverse effect on grain yield. The results strongly support the use of floodwater management and cultivar choice as methods to mitigate methane emissions from rice paddies.