Waterborne pathogens seriously threaten human life and can cause diarrhea, gastrointestinal disorders, and more serious systemic infections. These pathogens are usually caused by contaminated water sources that contain disease-causing microorganisms, such as bacteria, viruses, and parasites, which cause infection and disease when they enter the human body through drinking water or other means. Due to the wide range of transmission routes and the high potential risk of waterborne pathogens, there is an urgent need for an ultrasensitive, rapid, and specific pathogenic microorganism monitoring platform to meet the critical monitoring needs of some water bodies’ collection points daily monitoring needs. Microfluidics-based pathogen surveillance methods are an important stage towards automated detection through real-time and multi-targeted monitoring, thus enabling a comprehensive assessment of the risk of exposure to waterborne pathogens and even emerging microbial contaminants, and thus better protection of public health. Therefore, this paper reviews the latest research results on the isolation and detection of waterborne pathogens based on microfluidic methods. First, we introduce the traditional methods for isolation and detection of pathogens. Then, we compare some existing microfluidic pathogen isolation and detection methods and finally look forward to some future research directions and applications of microfluidic technology in waterborne pathogens monitoring.