During 1979-81, the U.S. Geological Survey conducted a large-scale study of the Apalachicola River in northwest Florida, the largest and one of the most economically important rivers in the State. Termed the Apalachicola River Quality Assessment, the study emphasized interrelations among hydrodynamics, the flood-plain forest, and the nutrient-detritus flow through the river system to the estuary. This report summarizes major findings of the study. Data on accumulation of toxic substances in sediments and benthic organisms in the river were also collected. Because of the multiple uses of the Apalachicola River system, there are many difficult management decisions. The river is a waterway for shipping; hence there is an economic incentive for modification to facilitate movement of barge traffic. Such modifications include the proposed construction of dams, levees, bend easings, and training dikes; ditching and draining in the flood plain; and dredging and snagging in the river channel. The river is also recognized as an important supplier of detritus, nutrients, and freshwater to the Apalachicola Bay, which maintains an economically important shellfish industry. The importance of this input to the bay creates an incentive to keep the river basin in a natural state. Other values, such as timber harvesting, recreation, sport hunting, nature appreciation, and wildlife habitat, add even more to the difficulty of selecting management strategies. Water and nutrient budgets based on data collected during the river assessment study indicate the relative importance of various inputs and outflows in the system. Waterflow is controlled primarily by rainfall in upstream watersheds and is not greatly affected by local precipitation, ground-water exchanges, or evapotranspiration in the basin. On an annual basis, the total nutrient inflow to the system is nearly equal in quantity to total outflow, but there is a difference between inflow and outflow in the chemical and physical forms in which the nutrients are carried. The flood plain tends to be a net importer of soluble inorganic nutrients and a net exporter of particulate organic material. Analysis of long-term records shows that dam construction in the upstream watersheds and at the Apalachicola headwaters has had little effect on the total annual waterflow but has probably suppressed low-flow extremes. Other effects include riverbed degradation and channelization which have to do with alteration of the habitat for aquatic biota and changes in flood-plain vegetation. Whatever management decisions are made should take into account the impact on the natural flooding cycle. Flooding is crucial to the present flood-plain plant community and to the production, decomposition, and transport of organic material from that community. Permanent, substantial changes in the natural flooding cycle would be likely to induce concomitant changes in the flood-plain environment and in the nutrient and detritus yield to the estuary.