The South Florida Water Management District (SFWMD), like many environmental management programs, is faced with complex decisions about research and management. These decisions incorporate both qualitative and quantitative information, are often characterized by uncertainty, and usually involve multiple decision makers. A decision analysis system has been suggested to help the SFWMD make such complex decisions. Through a case study, this paper explores the potential of the Analytic Hierarchy Process (AHP) as a decision analysis tool. The AHP is applied to the selection by the SFWMD Research Department of a water quality model for blue-green algal blooms in Lake Okeechobee. The three models under consideration were Eutromod, Expert Elicitation (structured scientific judgment), and WASP4. In the case study of model selection, four respondents were interviewed using the AHP. Three of the four respondents chose WASP4 as the favored model; this was an unexpected result for two of the respondents. WASP4's success was largely due to the emphasis the respondents placed on accuracy and the high accuracy rating this model received. The AHP was shown to be useful in finding the sources of differences in opinion. Thus, the AHP results appeared to be a useful basis for group communication and decision making. Based on the case study experience, it seems likely that the AHP has the potential to aid numerous types of complex environmental management decisions.