Public participation is an important way to improve the overall effect and social recognition of rural environmental governance in water source areas. Public participation makes environmental governance measures more targeted and effective, contributes to protecting the basic environmental rights of the public, and makes it easier to meet the livelihood needs of rural people. Public participation in rural environmental governance in water source areas is characterized by complex behavior and is dependent on public willingness to participate. Amongst other factors, it is subject to the combined influences of both internal (psychological cognition) and external (environmental regulation) conditions. This paper builds a theoretical framework for understanding public participation behavior in rural environmental governance, and uses it to analyze a case in the rural area surrounding the Xiqin Water Works in Fujian Province. In the case study, the public shows high willingness to participate, but low actual rates of participation. At the same time, the willingness of villagers to pay for the control of pollution from livestock and poultry breeding varies greatly from village to village, and there are also noticeable individual differences in public participation in the use of public collection points for rural household waste. We found that gender, understandings of environmental protection and perception of environmental regulation, play a key role in influencing the willingness of farmers to pay for the control of pollution from livestock and poultry breeding. Individual awareness of environmental protection, environmental protection facility conditions, and environmental service quality had a significant influence on public participation in the use of public collection points for rural household waste.