Photodegradation of chlorothalonil was studied in different natural waters (sea, river and lake) as well as in distilled water under natural and simulated solar irradiation. The effect of dissolved organic matter (DOM) such as humic and fulvic substances on the photodegradation rate of chlorothalonil was also studied in simulated sunlight. The presence of DOM enhanced the photodegradation of chlorothalonil with the exception of seawater. The kinetics were determined through gas chromatography electron capture detection (GC/ECD) and the photodegradation proceeds via pseudo-first-order reaction in all cases. Half-life ranged from 1 to 48 h. In natural and humic water chlorothalonil photodegradation gave rise to two different intermediates compared to distilled water demonstrating that the transformation of chlorothalonil depend on the constitution of the irradiated media and especially from DOM. The byproducts identified by GC/MS techniques were: chloro-1,3-dicyanobenzene, dichloro-1,3-dicyanobenzene, trichloro-1,3-dicyanobenzene and benzamide.