The accurate identification of the water layer condition of paddy fields is a prerequisite for precise water management of paddy fields, which is important for the water-saving irrigation of rice. Until now, the study of unmanned aerial vehicle (UAV) remote sensing data to monitor the moisture condition of field crops has mostly focused on dry crops, and research on the water status of paddy fields has been relatively limited. In this study, visible and thermal infrared images of paddy fields at key growth stages were acquired using a UAV remote sensing platform, and three model input variables were constructed by extracting the color features and temperature features of each field, while K-nearest neighbor (KNN), support vector machine (SVM), random forest (RF), and logistic regression (LR) analysis methods were applied to establish a model for identifying the water layer presence in paddy fields. The results showed that KNN, SVM, and RF performed well in recognizing the presence of water layers in paddy fields; KNN had the best recognition accuracy (89.29%) via algorithm comparison and parameter preference. In terms of model input variables, using multisource remote sensing data led to better results than using thermal or visible images alone, and thermal data was more effective than visible data for identifying the water layer status of rice fields. This study provides a new paradigm for monitoring the water status of rice fields, which will be key to the precision irrigation of paddy fields in large regions in the future.