A continuous field research effort has been carried out in the Apalachicola River estuary since March 1972. The information generated from this interdisciplinary study has been directly applied to the management of the Apalachicola resource by means of close associations among local, state, and federal officials and university scientists. During the early years, scientific data were instrumental in the prevention of the impoundment of the Apalachicola River. A series of regional studies was carried out to evaluate various forms of effects due to forestry activities, pesticides, and stormwater runoff from urban areas. A review was made of fisheries problems associated with dredging, overfishing, and marine pollution. Results of such studies were directly applied to local management questions. Research that linked the river wetlands with the estuary, in terms of the input of fresh water, nutrients, and organic matter, served as the basis for the purchase of extensive bottomland tracts. Other initiatives were carried out that were designed to protect the naturally high productivity of the river estuary. Further purchases of estuarine wetlands and barrier island properties were made that formed an almost continuous buffer of publicly held lands between upland developments and critical habitats and important populations of the bay system. A regional management plan was adopted that was designed to limit local municipal development in the estuarine region. Analyses of the long-term scientific data indicated that dominant, commercially important estuarine populations are associated with river flow, local salinity characteristics, and biological (predation, competition) interactions with the salinity regime and food web structure. Such interactions are not straight forward, however; they reflect complex interactions of the freshwater influxes and biological response in the estuary that are not well understood. Species-specific responses to the principal driving factors further complicate the biological relationships of the Apalachicola system. The management of a river-dominated estuary should be based on protection and control of freshwater sources, nutrients, and organic matter with a minimization of physical alterations that often lead to increased salinity stratification and the associated loss of the nursery function of the estuary. There is growing evidence that changes in upland characteristics and within-system habitat alterations are associated with changes in nutrient distributions and salinity relationships and that such changes can have serious impacts on estuarine systems. Issues involving basic changes in estuarine productivity and associated food webs are far more important than those involving species diversity in the management of such resources. Processes such as nutrient flow and salinity alteration underlie the very basis of estuarine productivity and usefulness. Over the past decade, there has been a gradual reduction in the importance of research as an integral part of the planning and management process in the Apalachicola system. This regional trend follows a national pattern. Dredging effects on the river and bay have gone on without effective challenge even though such activities are damaging productive habitats of the system. The once influential Apalachicola oyster fishery remains in disarray following a series of natural disasters and poor management practices. There is a growing problem with the deliberate obstruction of the generation and use of scientific data to determine management policies by various state and federal agencies. The substitution of public relations activities for the development of needed scientific information concerning factors such as the importance of sustained freshwater input to estuaries is further evidence that even the most elaborate and well-conceived management plans can be reversed by political manipulations and short-sighted bureaucratic policies.