The Plum Island Ecosystems (PIE) LTER is an integrated research, education and outreach program whose goal is to develop a predictive understanding of the long-term response of watershed and estuarine ecosystems at the land-sea interface to changes in climate, land use and sea level. The principal study site is the Plum Island Sound estuary, its coupled Parker, Rowley and Ipswich River watersheds and the adjacent coastal ocean, the Gulf of Maine. Humans are altering the ecosystems of the world at rates not previously experienced. Understanding and predicting how multiple stresses affect the sustainability of ecosystems is one of the most crucial challenges in environmental biology. The PIE LTER focuses on how several aspects of global change influence organic matter and inorganic nutrient biogeochemistry and estuarine foodwebs. The inputs of organic matter and nutrients from land, ocean and marshes interact with the external drivers (climate, land use, river discharge, sea level) to dictate the extent and degree of nutrient and organic matter processing and determine the spatial patterns of estuarine productivity and trophic structure. The overarching question is: How will trophic structure and primary and secondary productivity in estuaries be affected by changes in organic matter and nutrient loading and hydrodynamics caused by changing land use, climate and sea level?