Abstract: The water environment in rural areas is not only an important source of water for rural residents, but also closely related to agricultural production, sustainable development of rural economy, and farmers’ health. How to improve the water environment in rural areas has become an urgent and important issue to be solved. This paper integrates exogenous incentives theory and organizational trust theory into a unified analysis framework, using 962 household survey data from provinces such as Jiangsu, Anhui, and Shaanxi. Using the Double-hurdle model, the impact of exogenous incentives and organizational trust on farmers’ willingness to participate in water environment governance is empirically analyzed, and the mediating effect of organizational trust is explored to provide a reference for promoting good governance of village water environment. The research results indicate that firstly, exogenous incentives have a significant positive impact on farmers’ willingness and degree of participation in water environment governance. From a multidimensional perspective, both economic and emotional incentives have a significant positive impact on farmers’ willingness and degree of participation in water environment governance. Reputation incentives only have a significant promoting effect on willingness to participate. Secondly, organizational trust has a significant positive impact on farmers’ willingness to participate in water environment governance, but it does not have a significant impact on the level of participation.From a multidimensional perspective, goodwill trust has a significant positive impact on farmers’ willingness and level of participation in water environment governance. And competence trust has only a significant promoting effect on willingness to participate. Thirdly, a further mechanism analysis has found that organizational trust plays a positive mediating effect between exogenous incentives and farmers’ participation in water environment governance decision-making behavior. Based on the above research conclusions, this paper suggests that: firstly, village committees should improve the exogenous incentives mechanism for farmers to participate in water environment governance. The first step is to establish a credit system and punishment system for rural water environment governance, and moderately increase the performance rewards for public welfare positions such as river guards and cleaners. Then, the village committee should regularly carry out “Healthy Family” evaluation activities, actively promote exemplary models of protecting the village environment, and guide village social public opinion by utilizing farmers’ emphasis on personal reputation to enhance their sense of responsibility and honor and shame in protecting the water environment. Furthermore, the village committee should actively explore the unique customs and habits of the village, regularly organize collective cultural and entertainment activities to enhance the cohesion between farmers, and strengthen the relationship between the cadres and the masses to enhance farmers’ sense of belonging to the village. Secondly, grassroots autonomous organizations should strive to enhance their credibility. On the one hand, grassroots governments need to regularly carry out training activities on the professional abilities of village cadres, continuously improve their office skills, and establish a talent reserve system for village cadres to strengthen the organization’s talent team. On the other hand, the village committee should improve the “four discussions and two disclosures” system, standardize the procedures for disclosing village affairs information, safeguard the rights of farmers to know, participate, and supervise, in order to establish a fair and just image of grassroots autonomous organizations. Thirdly, the village committee should enhance farmers’ subjective awareness of public affairs participation. It not only needs to fully leverage the initiative of farmers through regular organization of courtyard meetings and the establishment of opinion boxes, but also avoids the formalization of grassroots election systems, in order to ensure the political participation rights of farmers and reduce their dependence on the government.