Estuaries represent a formidable challenge when it comes to determining status and trends in water quality, habitat, and ecological condition. These systems are dynamic and complex from hydrologic, nutrient cycling, and biotic resource perspectives. Hydrologically, freshwater runoff interacts with tidal saltwater exchange and upwelling, leading to complex circulation and mixing patterns. These patterns vary from minutes to weeks and meters to many kilometers, strongly shaping the chemical and biological characteristics of these ecosystems. In addition, there are strong seasonal and interannual shifts in climatic forcing (i.e., temperature, irradiance, rainfall, wind) that can vary substantially. Last, but not least, human activity is an additional and often dominant source of stress and change. At least half the world’s population resides in estuarine watersheds (Vitousek et al., 1997; Culliton, 1998), and this percentage continues to grow. Human development in coastal river basins has greatly increased nutrient and sediment loads to downstream estuarine and coastal waters (Peierls et al., 1991; Nixon, 1995; Paerl, 1997), resulting in deterioration of water quality, loss of fisheries habitat and resources, and an overall decline in ecological and economic condition of the coastal zone (Costanza et al., 1997; National Research Council, 2000; Boesch et al., 2001). Given the overall importance of estuarine ecosystems, there is an urgent need to develop sensitive, definitive, and broadly applicable indicators of water quality, habitat condition, biodiversity, and overall ecological change. The Committee on Environmental and Natural Resources (1997) summarized the need as follows: “To link stressors to biotic responses across diverse estuarine ecosystems, specific, yet broadly-applicable and integrative indicators that can couple biotic community structure to function in the context of ecological condition and change are needed