This paper describes a study of the treatment of 2,4-dichlorophenol (2,4-DCP) with an ethylenediamine-N,N-disuccinic-acid (EDDS)-modified photo-Fenton system in ultrapure water and different natural waters. The results showed that the EDDS-modified photo-Fenton system is adequate for 2,4-DCP degradation. Compared with a medium containing a single organic pollutant, the removal of pollutants in a more complex medium consisting of two organic compounds is slower by around 25 to 50% as a function of the organic pollutant. Moreover, 2,4-DCP can be further effectively degraded in the presence of organic materials and various inorganic ions. However, the photodegradation of 2,4-DCP in different natural waters, including natural lake water, effluent from domestic sewage treatment plants, and secondary effluent from pulp and paper mill wastewaters, is inhibited. Chemical compounds present in natural waters have different influences on the degradation of 2,4-DCP by adopting the EDDS-modified photo-Fenton system. In any case, the results obtained in this work show that the EDDS-modified photo-Fenton system can effectively degrade pollutants in a natural water body, which makes it a promising technology for treating pollutants in natural water bodies.