Coastal bays and estuaries are well known for their intrinsic recreational and economic value, yet these ecosystems are also among our most troubled natural environments. Urban development, agriculture, and shipping are just a few examples of human activities that can cause a wide range of deleterious changes within the coastal environment. These alterations, however, occur simultaneously with cycles of natural variability such as climate change. To effectively manage coastal ecosystems, we need to be able to carefully distinguish between anthropogenic and natural causes of change.