Agriculture accounts for the largest share of anthropogenic methane emissions. Rice paddy fields emit a significant amount of methane gas worldwide. Changing paddy water management practices has an enormous potential to reduce greenhouse gases. The clean development mechanism (CDM) project uses a market mechanism to reduce methane through private participation. There are various risks associated with private investment in CDM projects, although carbon credits as an economic incentive assist in mitigating some of these risks. Farmer participation plays a key role in the success of paddy water management projects in rural areas; however, despite the significant potential to reduce global methane emissions, very few projects have been implemented. When designing a Sustainable Development Mechanism (SDM) system, it is crucial to understand why the market mechanism in the existing CDM projects has failed. This study identifies and categorizes the risks and barriers to paddy water management in CDM projects and analyzes risk management options in CDM projects in India, Indonesia, and Mozambique. The results of this study showed that aside from economic risks, barriers to the application of technology in the field pose critical risks. The lack of knowledge and implementation experiences in rural areas increases barriers to practice. This in turn causes risk of difficulties in technology transfer which can be alleviated by improving awareness and introducing new knowledge through education and training in rural project implementation. Additionally, we highlight the importance of international efforts to build governance between the private and public sectors and promote technology transfers through multi-stakeholder engagement. This study provides specific information to encourage methane reduction worldwide and vitalize rice paddy water management in carbon reduction projects.