Rice fields are important contributors to the global methane budget. While rice production must increase to meet the demand from a growing population, there is a need to mitigate methane emissions through the employment of sustainable management strategies. A popular one consists of a short drainage that shortens the period of time spent in anaerobic conditions, but it is still unclear how drainage timing affects its overall effectiveness. Here we introduce a mechanistic model of methane emissions, coupled to the dynamics of redox potential and rice growth, to analyze the effect of a single drainage and the timing of its application on the temporal evolution of methane emissions. In particular, we identify the drainage timing that maximizes the mitigation efficiency of the drainage, defined as the reduction in methane emission relative to the emissions in continuous flooding. We also explore the role of organic amendment and show how it changes the optimal drainage timing. Application of this framework to a set of experiments demonstrates that emissions can be reduced by more than 60% if drainage is applied at optimal timing. The high efficiency and the limited negative effects on rice yields and N0 emissions place this water management among the most sustainable ones.