Photodegradation of crosslinked, hydrated polymer networks is an important lithographic process in the fabrication of structured biomaterials. In order to better understand the properties of materials fabricated using photodegradation, the process is mathematically modeled, paying special attention to how diffusible photoabsorbing species mediate the degradation of the polymer network. These light‐absorbing species may significantly alter light attenuation; thus, understanding the spatial movement of these species is critical in developing a predictive model of photodegradation. Using a series of mass‐action models, diffusion of absorbing species is shown to play a significant role in determining the final state of the photodegraded network. The predicted degree of degradation is significantly different when including the effects of diffusion than that predicted when neglecting diffusion. This model also explores degradation profiles that result from different experimental geometries. This model is the most accurate description to date of the relationship between experimental conditions and resulting photodegradation.