Estuaries exhibit a wide array of human impacts that can compromise their ecological integrity, because of rapid population growth and uncontrolled development in many coastal regions worldwide. Long-term environmental problems plaguing estuaries require remedial actions to improve the viability and health of these valuable coastal systems. Detailed examination of the effects of pollution inputs, the loss and alteration of estuarine habitat, and the role of other anthropogenic stress indicates that water quality in estuaries, particularly urbanized systems, is often compromised by the overloading of nutrients and organic matter, the influx of pathogens, and the accumulation of chemical contaminants. In addition, the destruction of fringing wetlands and the loss and alteration of estuarine habitats usually degrade biotic communities. Estuaries are characterized by high population densities of microbes, plankton, benthic flora and fauna, and nekton; however, these organisms tend to be highly vulnerable to human activities in coastal watersheds and adjoining embayments. Trends suggest that by 2025 estuaries will be most significantly impacted by habitat loss and alteration associated with a burgeoning coastal population, which is expected to approach six billion people. Habitat destruction has far reaching ecological consequences, modifying the structure, function, and controls of estuarine ecosystems and contributing to the decline of biodiversity. Other anticipated high priority problems are excessive nutrient and sewage inputs to estuaries, principally from land-based sources. These inputs will lead to the greater incidence of eutrophication as well as hypoxia and anoxia. During the next 25 years, overfishing is expected to become a more pervasive and significant anthropogenic factor, also capable of mediating global-scale change to estuaries. Chemical contaminants, notably synthetic organic compounds, will remain a serious problem, especially in heavily industrialized areas. Freshwater diversions appear to be an emerging global problem as the expanding coastal population places greater demands on limited freshwater supplies for agricultural, domestic, and industrial needs. Altered freshwater flows could significantly affect nutrient loads, biotic community structure, and the trophodynamics of estuarine systems. Ecological impacts that will be less threatening, but still damaging, are those caused by introduced species, sea level rise, coastal subsidence, and debris/litter. Although all of these disturbances can alter habitats and contribute to shifts in the composition of estuarine biotic communities, the overall effect will be partial changes to these ecosystem components. Several strategies may mitigate future impacts.