Water quality has evolved legislatively from protection of navigation routes and quantity of sources to more emphasis on impairments on water quality for surface and groundwater sources. Nonpoint or diffuse sources of impairments represents a major challenge for management due to the complexity of its sources and difficulty in tracking. The most cited sections on public policy analysis focuses on the overall process agencies employ to understand the results the program yields. Often overlooked are finer details and mechanisms, such as decision-making and priority setting, which have a great impact on the overall process. To investigate these factors, we need to analyze the decision-making process used by managers. This study focuses on using information from those with direct involvement in the establishment and implementation of the Total Maximum Daily Load program for the state of Florida. This study used decision-making analysis models from Rational-Decision-Making and Multi-Criteria Decision Analysis concepts to construct questionnaires that looks to develop priorities as seen by managers’ preferences for several presented options. This methodology allowed us to structure the viewpoints and processes water quality managers use to breakdown decisions. The analyzed results show water quality managers prefer strong management options, involvement from stakeholders with scientific knowledge, and data collected from the source or point of impact. Interestingly, opinions in the group show that urban best management practices are considered more effective than their agriculture counterparts with a disfavor for volunteer derived data. Ultimately, the survey highlights the need for more robust enforcement and reliable measurement of non-point source of impairments. Continued public outreach and education, especially through workshops, are denoted as important tasks to completing successful TMDLs and should be expanded and strengthened by both the Florida Department of Environmental Protection and its boundary programs.