Activities of man in rivers and their watersheds have altered enormously the timing, magnitude, and nature of inputs of materials to estuaries. Despite an awareness of large-scale, long-term changes in river-estuarine watersheds, we do not fully understand the consequences to estuarine ecosystems of these activities. Deforestation, urbanization, and agriculturalization have changed the timing and nature of material inputs to estuaries. Conversion of land from forest to almost any other land use promotes overland flow of storm runoff; increases the timing, rate and magnitude of runoff; and increases sediment, organic matter, and inorganic nutrient export. It has been estimated that total organic carbon levels in rivers have increased by a factor of 3-5 over natural levels. Man's activities have also changed the magnitude of particulate organic carbon relative to dissolved organic carbon export and the lability of the organic matter. Historically, rivers and streams had different features than they do today. Two of man's activities that have had pronounced effects on the timing and quality of river water are channelization and damming. Agricultural drainage systems, channelized and deepened streams, and leveeing and prevention of overbank flooding have had the combined effect of the amplitude and rate of storm runoff, increasing sediment load, increasing nutrient delivery downstream, and decreasing riparian wetland productivity. Dams on the other hand have altered natural discharge patterns and altered the downstream transfer of sediments, organic matter, and nutrients. Patterns of estuarine community metabolism are sensitive to variations in the timing, magnitude, and quality of material inputs from watersheds. The autotrophic-heterotrophic nature of an estuary is determined by three primary factors; the ratio of inorganic to organic matter inputs, water residence time, and the overall lability of allochthonous organic matter inputs. A simulation model is used to explore the effects of man's activities in watersheds on the spatial patterns of production and respiration in a generalized estuarine system. Examined are the effects of variations in the ratios of inorganic and organic nitrogen loading, the residence time of water in the estuary, the degradability of allochthonous organic matter, and the ratio of dissolved to particulate organic matter inputs. Simulations suggest that the autotrophic-heterotrophic balance in estuaries is more sensitive to variations in organic matter loading than inorganic nutrient loading. Water residence time and flocculation-sedimentation of organic matter are two physical factors that most effect simulated spatial patterns of metabolism in estuaries.