Glyphosate is the most widely used herbicide in global agricultural cultivation. However, little is known about the environmental risks associated with its migration and transformation. We conducted light irradiation experiments to study the dynamics and mechanism of photodegradation of glyphosate in ditches, ponds and lakes, and evaluated the effect of glyphosate photodegradation on algae growth through algae culture experiments. Our results showed that glyphosate in ditches, ponds and lakes could undergo photochemical degradation under sunlight irradiation with the production of phosphate, and the photodegradation rate of glyphosate in ditches could reach 86% after 96 h under sunlight irradiation. Hydroxyl radicals (•OH) was the main reactive oxygen species (ROS) for glyphosate photodegradation, and its steady-state concentrations in ditches, ponds and lakes were 6.22 × 10−17, 4.73 × 10−17, and 4.90 × 10−17 M. The fluorescence emission-excitation matrix (EEM) and other technologies further indicated that the humus components in dissolved organic matter (DOM) and nitrite were the main photosensitive substances producing •OH. In addition, the phosphate generated by glyphosate photodegradation could greatly promote the growth of Microcystis aeruginosa, thereby increasing the risk of eutrophication. Thus, glyphosate should be scientifically and reasonably applied to avoid environmental risks.