The study examines the application of modeling photochemical processes in natural water systems. For many photochemical reactions occurring in natural waters, a simple photochemical model describing reaction rate as a function of intensity, radiation attenuation, reactant absorptivity, and quantum yield is insufficient. Other factors governing the species distribution must be considered. These factors are divided into processes that cause production, decay, and mixing and transport. Three different photochemically active compounds are used as examples to illustrate how these various factors affect their distribution. Hydrogen peroxide is used as an example of a compound that is produced in situ, whereas trifluralin and pentachlorophenol are compounds that have very different absorption spectra and are introduced from external sources.