A limited number of research trials have been reported in the past to model pathogenic organisms in streams and large water bodies at a watershed scale. In this paper, modeling of fecal coliform in streams is proposed from a management perspective at the watershed level. To model the fate and transport of fecal coliform in a watershed in Southeastern Kentucky, an object-oriented (OO) simulation model, based on the concepts of system dynamics (SD) approach, is proposed in this study. The approach combines both data-driven approaches and insights gained from a process-based approach. Different management scenarios, based on flow conditions and pollution sources, are generated and evaluated to validate the proposed approach. Deterministic and conceptually simple probabilistic analyses are carried out to understand several water quality management alternatives that aim to reduce pollutant loadings. Results point to the potential use of the proposed OO–SD framework in addressing environmental policy issues and also to the need for relying on probabilistic analysis to obtain more credible results and recommendations in data-poor conditions. The proposed approach helps direct limited funding and watershed management efforts to be focused on areas that have the greatest impact on the surface water quality conditions.