A conceptual model of pathogen-specific hazards in pit latrines over time is presented. The development, limitations, and results of an illustrative application of the model are reviewed. Literature reviews were conducted to determine the required model inputs of each reference pathogen included in the illustrative application. Findings of the reviews are included. Results of the illustrative model application indicate hazard reaches a steady-state equilibrium and the majority of cumulative hazard for a two-year latrine use period is contributed in the most recent month. As a result of these behavioral trends, we found manipulating pit emptying frequency (or pit fill rates) and utilizing double pit technology could have large impacts on the relative hazard posed by a community’s pit latrine waste stream. Our model also provides evidence that unless sewerage with wastewater treatment is of relatively high quality, it may be no more effective than properly managed pit latrines at reducing pathogens.