Based on a comprehensive review of domestic and international research progress regarding the source distribution characteristics, migration and transformation mechanisms, ecological and environmental risks, and main removal methods of typical emerging contaminants (including pesticides, antibiotics and antibiotic resistance genes, microplastics, and per- and polyfluoroalkyl compounds) in agricultural ecosystems, this study investigates the impact of changes in farmland irrigation and drainage conditions on the transport of emerging contaminants. The study proposes that future research should strengthen the whole-life cycle monitoring of emerging contaminants in agricultural ecosystems to accurately identify the sources, types, distribution patterns, and concentration levels of typical emerging contaminants. Particular attention should be paid to their transport, transformation, and bioaccumulation effects during different crop growth stages and through farmland irrigation and drainage systems. Further understanding should be developed regarding their accumulation and transformation processes in the water-soil-crop system and associated ecological risks. Additionally, an applicable technical system for emerging contaminant removal should be established by integrating with farmland ditch and drainage engineering. These advancements will provide technical support for the prevention and control of emerging contaminants in China’s agricultural systems, ensuring regional ecological security and promoting high-quality green development.