Throughout the watershed modeling process, modelers, collaborators, and stakeholders make decisions about how to study various challenges that impact watersheds. To understand these decisions, we investigated values held by modelers who have worked or collaborated on projects within the Chesapeake Bay Watershed and their influence on decisions made during the modeling process. Using a mixed‐methodological approach, we designed an online survey and semistructured interviews to evaluate these complexities. In total, we received 27 survey responses from Chesapeake Bay Watershed modelers and conducted four semistructured interviews. The results indicate that ethical and epistemic values impact every stage of the watershed modeling process. These values occur alongside decisions, motivations, outcomes, and objectives that often involve collaborators and stakeholders in addition to the modelers. Therefore, including these values in scientific discourse can increase transparency around watershed modeling that guides policy decision making processes. Our results articulate that a discussion of the ethical and epistemic values present throughout the watershed modeling process should be incorporated into model documentation to clearly explain assumptions and decisions.