Abstract: Water resources are crucial for environmental protection and the health of humans, plants, and animals. Contamination of water by pathogens such as bacteria, viruses, and protozoa can lead to outbreaks of various water-related infectious diseases, posing serious threats to public health and causing significant economic and social losses. Therefore, accurate and timely detection of pathogens in water sources and related substances is vital for preventing water-borne infectious diseases. In recent years, various molecular techniques have been extensively used to address water quality issues, including emerging isothermal amplification techniques such as loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), recombinase polymerase amplification (RPA), and helicase-dependent amplification (HDA). These techniques have significantly enhanced the capacity to detect and monitor pathogens in diverse aquatic systems and wastewater. This review focused on commonly used isothermal amplification techniques in water quality assessment and their recent advancements in environmental pathogens detection.